I use one project just for mastering backing tracks for live play, for leveling etc. Hundreds of them. The workaround I use for your problem is I move each track to the same finish point, so that all tracks are essentially the same length. Then for bouncing out, just select the track I want out, and it bounces out from the beginning of the selection to the end. I have a marker set for the last 'crash' or note of the track, for alignment.
Works well, although I'm sure there is a better way.
Dave