You can do just about anything you want. I complain a lot about DVDA 2.0, but under the covers, the SoFo engineers added quite a lot of good stuff compared to 1.0.
I just did the following, just to make sure it works:
1. Start a new "Menu Based" compilation (that's right, not a Music Compilation).
2. Right click on the main screen (where it should say "Menu1" at the top) and select "Insert Music Compilation" from the pop-up. This should insert a button labeled "Music Compilation 1."
3. Double-click on the music compilation button. The center of your screen should now show "No Songs to Display," and the right side of the screen should be asking you to drag and drop audio files. If it doesn't, make sure to select the "Compilation" tab rather than the "Properties" tab.
4. Drag your various MPEG-2 files (I know it says drag "audio" files, but drag your video files instead) into the Music Compilation area on the right of the screen. Before you do this, make sure that your AC-3 files are named identically the same as your MPEG-2 files (with the extension AC3 instead of MPG) so that DVDA will "discover" the audio that matches your video.
5. On the left side of the screen, double click on the main menu to get back to the first menu. Right-click on the button you created when you inserted the music compilation (the one labeled "Music Compilation 1") and select "Insert Scene Selection Menu." This will insert the chapter points for each of your videos.
Now for the limitations. You cannot add more chapter points -- the only navigation is to the beginning of each MPEG file. Also, if the audio is different for any of the MPEG files, the audio will have to be recompressed to match whatever default you set for the project.
I had thought about adding an extra menu to recreate the compliations and link to it, leaving the original to just end and return to the menu. I think that should work. Unfortunately the clips are not mpegs yet - just .jpg files - loads of them! However, I think the concept may just work exactly the same.