I'm pretty sure the example in this article wouldn't confuse git: weirdness like this is the reason git has the "recursive" merge algorithm instead of just doing a plain three-way merge. A recursive merge basically tries to merge some of the parents together before doing the final merge, which resolves this sort of case.

I do criss-cross merges between git branches all the time with no ill effects. Maybe non-git VCSes can't handle this sort of thing.