I looked into this a while ago too, and eventually gave up. I made a family friendly edit of the Robot Chicken Star Wars DVDs and wanted to have 2 options: The whole she-bang, and a shorter playback list including just our favourite skits.

It seems like I had a decent premise because I essentially had the full video file (ABCDEFG) and occaisonally just wanted to play part of it (ACEG). If you did your thing with the adverts, I think you would structure your video file like this:

MF=Main Feature, A=Adverts A, B=Adverts B

MF1 A1 B1 MF2 A2 B2 MF3 A3 B3 MF4

Playback one would be MF1--MF2--MF3--MF4

Playback two would be MF1A1-MF2A2-MF3A3-MF4

Playback three would be MF1-B1MF2-B2MF3-B3MF4

There will be some seek time at any change, but it should be relatively low (even on a DVD9) since you're always seeking 4 or so minutes into the future (8 maybe, on the advertless one) and not to some random part of the disc.