Literally my thoughts and I was gonna make a post about this exact observation but you beat me to it by *checks calendar* A WHOLE YR lmao😭i left this manhwa to marinate and just got back to rereading it and wanted to add onto this analysis!
I believe Ludovicas final words to Johannes heavily influenced how he ended up handling everything concerning Shuri and how he ends up treating her horribly during mental episodes when his illness gets worse.
Ludovica was (this is the way I interpreted her and her actions) greedy when it came to her future and relationships with others.
When Johannes finally confesses and she sees the truth for what it is, she gives him an ultimatum, not words of regret or hope, or any sense of comfort or realization. She suspected his feelings long ago yet when he didn't have the courage to face her and tell her the truth, she moved on and went for the greater prize/outcome (the emperor, his friend). It was HER WAY or the HIGHWAY. She even coveted a rose that she knew he had because of her. His love wasn't enough and it would never be if he wasn't willing to lay everything down for her.
Anyways, back to my point: Ludovica's harsh words and craving to have it all was so strong that Johannes slowly becomes just like her with his new fixation on Shuri, which is ironic considering how much he adored her and how he hated feeling during his final interaction with her (Ludovica).
I believe that she didn't have eyes for the emperor, nor did he have any for her until Johannes' feelings became obvious and he didn't make a move. It's almost implied that she slowly curried the emperors favor (seduced him), because he was going to marry the current empress up until that point and her actions complicated things and changed the outcome. Which is also why currently the empress and emperor are still on rocky terms.
Ludovica was never really a loving or caring person, because in the end she was gonna get what she wanted at whatever the cost may be.
Johannes is quick to find out everything about Shuri and marry her, because as has been proven in the past, if he misses his opportunity he will regret it and never get another one like it again.
So he snatches it up and keeps it in his grasp, sometimes loosening his hold when things seem to be alright and calm (moments where he teaches Shuri about her future duties and just getting along with her in general) and at other times he crushes his hold so tightly he harms her (the flower) in the process (his creeping doubts becoming too big to ignore and leading him to confronting her and physically harming her/the necklace incident).
There's even a panel of a lion, clearly acting as a stand in for him, that showcases focused eyes, indicating that he's on the hunt rather than caring about Shuri's situation when he tasks the knight to find out about her.
In the end, he knows what he's doing and how insane it must be that he acts this way, yet is still met with her gentle smile and kind demeanor, a direct reflection of how Ludovica cruelly treated him and how he could only ever respond/react mildly to the situation at hand because of the image he so firmly holds of her in his mind. Ludovica was never like the woman he longed for in his mind.
He constantly projects his updated image of Ludovica onto Shuri (immediately thinks she's scheming and conniving , just like Ludovica, when the necklace incident occurs) and its why he's so reactive and violent.
He literally grooms her to be the perfect wife (everything he thought Ludovica should be like) but that later changes as he gets closer to death and prioritizes grooming her to be the perfect head of household instead.
Despite knowing that they aren't the same person and that she's long gone he continues to have unkind moments with her, and this is probably the closest he gets to knowing how Ludovica felt having power over him.
It's also why he feels horrible for what he'd done and seeing how she is just like how he was towards Ludovica, quick to forgive because this was one of the few times he was ever a bad person to her and the good outweighed the bad in their eyes.
I think Ludivicas' cruel nature and sharp words affected him so much that he never forgot about them, burying them deep, until they resurfaced later in his life. She still held power over him and what might've once been a pure love was now tainted and unwilling to let him go.
What I really think is that he had been so psychologically damaged by her emotional manipulation of him and it depicted her emotional abuse of him, which then started a cycle of him being the same towards Shuri until she broke it/forgot about it but she didn't leave unscathed by the effects of it (ptsd). The abused becomes the abuser.
Ludovica is not a manifestation of his love or regrets or anything of the sort, at least I don't think she is. She was abusive and toxic and left a mark on him and held him hostage in his final days. A very clear depiction of how victims will never forget their abusers or what they'd done to them. That despite having a loving family and things to live for it just wouldn't leave him alone and he was in denial over the reason it clinged onto him after all those years.
She was also implied to have not been a good person in general judging by the fact that the palace has no clear records of her or anything that she'd done in her time in the palace when she was alive. I think this is also a reason why the emperor makes up with the empress and finally decides to forget about her, he saw that she wasn't who he thought she was and will not be the one to be hung up about it.
All in all, I like that this part of him was heavy and does a good job of showing male victims of abuse. However, I would like to add that this does not justify his actions towards Shuri. It's an explanation as to why but it does not excuse it.
I was lowkey pissed that this is how Ludovica haunted the narrative and how she was the catalyst to Shuri's suffering, but I will not discredit Johannes part in it, as he's the adult in the situation and was the one who triggered the series of events that started off the story.