none said:

The goal is to take a TV recording and have a playback option which skips the commercials. Possibly might have a third option which will offer up a second set of commercials instead of the original ones.

Why do you need the commercials? Is it nostalgia? I have no experience with seamless branching. Instead, if I were you, I would:

1. Edit out the commercials for the main feature, in your editing program.

2. Make the original commericals into a video featurette. Make another featurette with the alternative commercials.

3. Author a DVD with the main feature, and add two extras: original commercials featurette and alternative commercials featurette.

That way you could edit without having to worry about seamless branching, avoid compatibility problems and preserve the commercials. Just a thought!