Can I upgrade brakes despite interface difference
In my experience, the gap there isn't a problem.  Usually those "long" spring ends go all the way through the brake mounting plate and a bit out the back side anyways, so there isn't an issue if they are a little shorter.  As for the gap on the v-brake mount on the bike, too short is an issue.  Too long usually isn't.  As Criggie says in the comments, fantastic job on the photos showing the exact issue.  But as long as the Shimano brake's spring end goes through the hole in the mounting plate(and doesn't back out of it) and the brake moves freely with the mounting screw tightened, you should be good to go.