i feel the same! Alisa/Damon is like this natural course in all other routes but Damon's. they talk in his like they're a thing of the past, and that would work if that continuation was there in all routes, but instead they def still have a thing going on. it's like Damon's route is an alternate dimension where he and Alisa's feelings are strictly platonic. but.. that's not the case for the other routes so like you said it feels less real.
i think there being personal relationships or just a possibility of more between crew-members (like w/ Bash & his crush on Ryona) is cute and adds character building. but since MC can be romantic with any one of them the idea of anyone already being "involved" makes any relationship MC forms with them less solid
i have no issue with Damon and Alisa having been a couple in the past regardless of the route, but it's the way it's dismissed as being over in his route but still a present relationship in the others that's seems spotty