After having a poke around this morning, it looks like I've also worked on games with fairly large audiences that give focus to whatever the mouse has hovered over (such as Day of the Tentacle Remastered or Hand of Fate) and I don't recall anybody having trouble with those, so I don't think that any negative impact is likely to affect a wide range of people (that said, I haven't come across anybody who's had problems with the sort of thing I did here in Cloud Courier before either).
In the game where I had a blind user experience problems (the Bonesweeper prototype), I added an option to disable mouse input and set a couple of other blind-friendly settings all at once, but I think the broad conventions of keeping focus and hover as separate states for normal GUI widgets is important - in general, a lot more usability/accessibility research goes into general GUI toolkits and standalone applications than games, and that feels like a good lead to follow :D