You should be using NTSC DVDA template if its going to be used in DVDA. That doesn't affect video quality just if the audio is muxed in or not. I think the straight DVD template produces elemental streams which DVDA cannot use. The DVDA template produces a file with audio but nothing in it. That's why you also need to render out the audio and the DVDA muxes the two together when you do the prepare DVD process. This isn't re-encoding the data, just merging it.

Sorry if that wasn't a very technical description.