Alright, I get your reasoning, here's my counteroffer (this is me spitballing and spending like two hours to come up with a concept, feel free to veto any of this, it's basically just headcanons (I don't wanna overstep any boundaries 🙈)):
Andy doesn't tell Remy but does tell or is found out by a seelie monster friend of hers - someone who is barely a monster or kinda human passing and therefore not someone Andy is as biased against. Let's call them Leaf for now.
Leaf manages to convince Andy not to tell her family about the pregnancy and to stay away from monster hunting. They will help her through the pregnancy instead and while Andy is reluctant, she agrees. During the pregnancy and around the first three years of Virgil's life, Leaf slowly helps Andy work through her biases - not all of them but most. She still isn't willing to tell Remy and is very wary of the Royal Family as well as Claims (whatever her opinions are exactly, it might soften but not disappear.) She does have an easier time loving Virgil though (this is assuming she had a hard time with it in the og timeline, idk.)
Virgil grows up more cared for, though a bit isolated. He gets homeschooled and mostly interacts with Andy, Leaf and a few other monster/monster-friendly friends (maybe some of them have kids Virgil can be kinda friends with but nothing super close.) Andy doesn't take him to other realms and she doesn't want him to learn fae either (though Leaf teaches him a few words here and there.) He is told a bit about Remy - that he's half-drider but a good guy and that Andy made the choice of not involving him in his life so far (with various justifications he might or might not buy into) - but doesn't meet him until he's 10.
That's the age where Leaf convinces Andy that Virgil is old enough to make the decision himself. He has been trained in magic to protect himself in both mind and body and has shown talent, so Andy knows he can defend himself at least a bit. Virgil is hesitant but does want to meet his father.
Leaf arranges a meeting between Remy and Andy, though they do not tell Remy what it's about. As far as Remy knew, Andy had some family issues and had to disappear for a while (so he wasn't ghosted but didn't know the full story.) Andy tells him about Virgil but puts heavy conditions in place for him to be able to meet his son. Which include that he's not allowed to be alone with him for now (Andy has to be present the entire time (she is mostly over the eating thing but there are also a lot of things she doesn't want him to tell Virgil, for example about Claims)), that Virgil isn't allowed to get involved with the seelie royal family until he's an adult and wants to meet them, etc. Remy is not happy about that but after long negotiations he agrees to most of them (there might be magic involved to make sure he sticks to it). He does insist though that Roman is exempt from the 'no contact with the royal family'-rule, even if their meeting will probably still be a few years down the line. Remy and his family live a long time and Virgil is - according to Leaf (who Remy trusts a bit more) - already showing potential to become a powerful witch, so he should live long as well. There's time for him to meet everyone, even if Remy is an impatient bitch. It's better than Andy breaking off contact again and keeping his son from him indefinitely.
So Remy and Virgil meet and Remy immediately loves him so much. They bond quickly - mostly through clicking and Remy teaching him about his drider silk. Remy stays for dinner and after a talk with Leaf discovers that Virgil apparently ate more than usual. As in, Virgil still adjusted his eating habits to Andy and Leaf even without being reprimanded for eating too much, though he still eats more than in the og timeline. Remy makes sure that his visits always include at least one meal, though Leaf also promises to make sure Virgil knows that it's okay for him to eat more. He does get better in this timeline and doesn't have an eating disorder once he grows up.
Remy gets more involved in Virgil's life, though Andy doesn't let them be alone with each other until at least a year later. That is also around the time when Virgil gets a phone and they can message each other online, away from his mother's eyes. I think Virgil would love Andy as his mother and still be influenced by some of her biases, so he is a bit scared of the seelie royal family. Andy has a very negative perception of them, Leaf is very neutral and Remy is very positive, so Virgil isn't entirely sure what to think. So he relies on the knowledge that they are all very powerful and that politics are complicated and dangerous, so he agrees with his mother to wait to get involved with them until he's older and more powerful. Remy tries to convince him otherwise, but he can't argue that there is some logic behind the argument.
Roman enters the picture when Virgil is about 14/15. He and Andy do not get along well, especially since she insists, same as with Remy, that she'd be there the entire time he meets Virgil. Virgil, now fully in his teens and a bit rebellious, is annoyed by it too, but also still somewhat intimidated by Roman's position as Crown Prince, asks Roman to train him. Andy is furious but Leaf talks her down, saying that it's a great opportunity. She reluctantly agrees but Roman has to make her a few promises (very begrudgingly on his part), mainly about not hurting Virgil, respecting his boundaries and not taking him to the fairy realm until he's of age and agrees to it.
Virgil grows quite powerful under Roman's guidance. He's already been learning a lot of magic from Remy and Leaf (idk what Andy could contribute, since she's known to be a disaster and bad at her job but I think she could at least teach Virgil most of the basics of both combat and magic) and with Roman's combat training, he feels more secure. Still, he has anxiety in this timeline, too, so he's still reluctant to meet the rest of the royal family well into adulthood. (Though I think he does have contact with Remy's parents earlier, whether that is online or they come to visit. Virgil does not go to the royal palace yet.)
Virgil is training with Roman when Roman is informed about Janus' capture. Of course, he immediately wants to leave and Virgil - who has been learning fae but is far from fluent and was looking for a way to prove to himself and his family that he's powerful enough and ready to dive into fae politics and meet Roman's family - insists that he takes him with him. Roman is very reluctant (Remy will kill him if anything happens to Virgil) but Virgil manages to convince him (maybe there's favors involved, idk) though he is assigned bodyguards by Roman and isn't on the front lines. So Virgil joins the campaign, without his parent's approval (he is an adult though, so... they can't really tell him no. They are still furious when he gets back.)
They end up finding the prison where Janus is held only just before the Unseelie. Roman and his cavalry hold them off while Virgil's in the unit that go to free the prisoners and get them out before the Unseelie can get to them. The prison guards have already fled like in the og timeline. Virgil ends up freeing Janus again, this time communicating in broken fae and maybe still a bit of magic. On their way to the fairy circle, they are attacked by some Unseelie that managed to get inside but Virgil manages to fend them off, impressing Janus - who at this point doesn't know he's Remy's kid since he knows Remy would never allow him to be here. Anyway, they manage to make it back to circle and the seelie royal castle where Remy is already waiting, ready to chew out Virgil (and Roman for letting him go with.)
And that's basically my justification on how Virgil can still end up with Janus 😋 I'd guess afterwards, Virgil decides to stay in the castle and gets rewarded for his efforts. Idk how Andy will react or if she and Virgil still have a good relationship at that point... This is just a very vague idea of what could happen and I definitely took way too long to think this up 😂
That's one hell of a headcanon! Wow, you put a lot of thought into this! Sorry it took so long to respond, the super long ask was a bit intimidating >.<
Leaf being part seelie/seelie monster alone would endear them to Andy more than Remy bias-wise. The problem isn't so much about Remy being human-passing as it's about what he is.
I still say that Remy wouldn't let anything keep him from his son and keep him from introducing him to the royal family, and he would have the entire seelie royal family backing him up so that's kind of a plot hole, but feel free to ignore that. Sometimes it's fun to get a little out there with headcanons and this is a good one!
Still including the eating thing is sweet. It gives Remy something to help Virgil with.
To be fair, even other fae are afraid of the royal family, so it's completely valid for Virgil to be afraid of them.
I can't see Roman promising Andy anything. There's too much that can go wrong with a promise. He may tell Andy that he won't do certain things and she'll have to believe him because he can't lie and just trust that he won't change his mind, but I don't think promises will be on the table.
This is a good idea! I like it a lot! It's sweet and gives Virgil a chance to have a good relationship with his mom while still getting to fall in love with Janus. I also like the addition of Leaf, I didn't even think of adding a new character to make it work! Very creative, love it.