You're correct…one disk per video in Compressor.
Offhand, you could take your videos as clips into FCP or QuickTime Pro and make a single sequence and put chapter markers at the start of each of the three. Should work.
BTW, the markers are added in the Preview window of Compressor.
As for Toast, I don't use it but from what I know of it, I don't see why it couldn't easily do what you want.
If you compare, I'd be interested which workflow works best.