I just realized something with my above post; that's already the way it works. so, in light of that, here's four more suggestions that shouldn't make me look like a dumbass
first: one-way Raft paths. in my game, I have a "current" that takes Link on a somewhat scenic trip through a part of an area, but the problem is, Link can get right back on his raft and go into the current. having raft paths that disable movement in one direction would fix this completley
second: a Misc/Weapon sprite for the raft, to display it from more angles. the graphic would flip horizontally, but not vertically, because that would look funny if the sprite was drawn at a perspective
third: stop Link's animation on the raft
and fourth: make trigger combos trigger when Link passes over them on the raft. that could make some very interesting water puzzles if used with the first suggestion, and Raft Branch flags