This has been a problem for some time, but I think I might have an idea of how to fix it. Basically if Link's center is within a certain distance of the combo's center it should trigger the raft and override drowning. If this is something that would work for you guys, let me know.
Docks and Drowning Water (Possible Fix)
Well, in Zelda 1 I've never drowned when walking onto a dock, so sounds like a good solution to me.