When you see there is more than 1 title in the Main Movie, you're going to have to preview it anyway if you intend to choose only one of them. Instead of previewing it in DvdShrink, play the original with a software player, going through the menu selection to see which version you want. Then take note which title it is playing and select it accordingly in Shrink.

Alternate versions are actually interleaved and either have seamless branching (i.e. you cannot switch between versions while playing on one version) or multi-angle (i.e. you can switch between versions while playing) involved.