Hordak is Hades and Entrapta is Persephone
Okay first off, I don't really have anything insightful here I just kind of thought that Entraptak kind of has Hades/Persephone vibes? But not like the classical Greek mythology version of it (although well, maybe a little) but more like the Lore Olympus version of them. Kinda. Sorta. Maybe.
So Entrapta is not originally from the Fright Zone, which is Hordak's domain, but she inexplicably got herself stuck there. And in this environment which should be harsh and alien to her, she actually thrives really well. She is really within her element there with all the technology that they have, and adapts to it in a short amount of time.
This is sort of how Persephone was in Lore Olympus as well. When she first visited the Underworld by 'accident' (it was a bit more than that but you know, we'll just leave it at that), she was scared but she really quickly acclimated herself pretty well there, especially when she was dealing with Cerberus. And when she starts working for Hades that's when she really starts to get comfortable, and start to develop her powers and reach her full potential.
And both Hordak and Hades played a role in Entrapta and Persephone being able to reach their full potential. They were both in positions of power over the other, for sure, but both Hordak and Hades had great respect and admiration for Entrapta and Persephone and trusted their judgement. It was this trust that I believe both female characters had not really been given by their friends/family/peers.
For Persephone, it seems that the Olympians didn't trust her simply because she was young, and also her mother was overprotective of her. But from the moment that Hades met her, he didn't talk down to her despite their age difference (and Hades was still careful to not present himself as fully one of her peers of course because he was aware of the power dynamics), and it must have been the first time that Persephone felt like she was given respect from an adult. And this respect and trust continues as the story unfolds.
For Entrapta, she is certainly older, but I got the feeling (and this can just be my interpretation) that the other princesses kind of felt like she was too 'offbeat' and perhaps acted 'too young' (probably on account of her neurodivergency) and so they didn't ever really trusted her to do things unsupervised. But Hordak immediately recognized Entrapta's skills and knew that she should be given the freedom and independence to do the experiments she wants to with access to the resources that the Fright Zone has at its disposal.
And another way that Hades and Hordak are similar is that both men sort of approach their "work" in similar ways. They both feel that they do it out of a sense of obligation. They take pride in what they do only when it is done well and done properly. And both of those attitudes seem to stem from trauma related to a father figure that saw them as something that was "in the way" of their power. I think that maybe what they (Hordak and Hades) see in the types of characters like Persephone and Entrapta is that the two women both have a passion and an optimism that comes naturally to them, and are also extremely talented as well. Instead of seeing it as a threat, they instead want to nurture this passion and help them reach their full potential.
Because of the trust, respect, and independence that is granted to our respective female characters, they also use their skills to help the more powerful male character in return. Not because they were ordered to, or because they felt like they were forced to, but because they genuinely want to help.
tl;dr, I just think both relationships are really good/healthy ones, even quite aspirational. I don't think they're problematic, even if they started off with uneven power dynamics. Maybe we should try to see how the relationships develop and actually focus on what happens between the two characters rather than simply label something as "problematic" and leave it unexamined.
(And besides, as someone who's OTP is actually problematic I think I know what is a problematic ship when I see one)