I know I've said that before.
The best seamless branching is just you asking the DVD to skip or rearrange certain chapters in the film. It'd be very easy to put both versions of the ending there, and set it so that the alternate can be played.
Again, I would edit the film with the "S-Mart" ending, and then place the "Apocalypse" ending after the credits. Selecting the S-Mart ending, the movie will play normally without any weird editing/branching glitches. Selecting the Apocalypse ending, you'll try to make it fit into your edit as seamlessly as possible (cutting the chapter mark on the same frame the "S-Mart" chapter also begins), although there will still be slight differences or glitches depending on what player is playing the edit.
For the rest of the edit, don't fiddle with seamless branching, it'll make a mess of your edit. Just choose your favorite version of each line. Although I suppose you could also do an alternate sound mix, which wouldn't necessitate any weird branching fiddleypoo.
Party on.