I kinda figured that Damon and Alisa being viewed platonic in Damon's route was for the comfort of people who would rather focus on romancing Damon than the idea of Damon ever having been with anyone previously, or some past flame appearing out of nowhere to cause drama.
I don't think it'd make it less canon that Damon and Alisa happen to be into each other in every other route and not Damon's route, because isn't it just a part of life to have that "what if" relationship play out in every other scenario than the one that's currently happening in 'Canon'?
That's only my thoughts on it though, I understand that not everyone's going to be comfortable about the whole side character possible romance subplot happening in the background.