It's not just Eliza, although as the main partner, it is much more prevalent than with the others. It's every LI, the dialogue is written on the assumption you take every girl every time. If you don't, it gets weird. And if you don't like Eliza, then you will struggle. I can't remember the post, but Dev was very clear there would be a lot of Eliza.
I am doing a solo Eliza path (and might do other solos depending on how they develop) plus a harem path with taking everyone so far (except Kira & Alice, I just don't like them). And apart from actual sex scenes there is no difference to the paths.
I thought once we hit "major choices" that it would fix it and turn the romance off, but that only appears to take out choice and force you to do stuff. I did a 'major choice' to not pursue Kira, yet later had the option to have sex with her (and her trust is negative too). Alice is another one, I have repeatedly said no, no, no. And was curious, so I said yes once and I'm getting a BJ. I found that a bit weird.
I also think MC might be a bit bi-polar. Have the chance to be angry at Kira a couple of times for her betrayal, and then suddenly. I trust her. I've turned romance option down every time, yet MC is sitting there saying I need to work out how I feel about Kira. I've said no 11 times, I think that's a big enough clue.
Don't get me wrong, not bashing the game, I love it. It's still among my very favorites, but I think the dialogue pathing is very weird if you're not fucking everybody.