I agree, it also removes some of the sandbox aspects, that you can fuck and cheat to the player's desire, within reason, from the game.
I suspect that perhaps Eva feels there are too many variable states surrounding Ian/Lena/Holly so she is restricting accessibility?
I guess that for those characters, as EvaKiss envisions them, the logical consequences would affect the story too drastically and their relationships being at the very least amicable is necessary to keep the plot functional.
I think something that gets a bit overlooked are the implications for Holly's character if the scene with Lena were to happen while Lena and Ian are dating. Like, the player can make Lena's character be very hypocritical (in particular with what she might be trying to do with Jeremy), so in that sense I don't think it would be
too out of character for her to go after Holly, but would Holly accept her kiss after being made aware in chapter 8 that Ian and Lena are indeed dating and starting to get serious? I feel Holly as a character wouldn't do that, she's too sincere and wouldn't want to be complicit with Lena cheating on Ian, and things would be very awkward for the character dynamics if she had to refuse Lena.
So my guess is that's why EvaKiss just straight up blocked the decision if there is a set relationship between those 3 characters, not because proposing at that point would be too out of character for Lena, but because it would put Holly's character into an impossible situation that would affect too many story threads.