I think you're right with the latter, a volume boost will always make something sound better in an A/B. I think the re-mastering itself has far greater impact than which format you're listening to it in, even the cd (kept in my car) sounds fantastic...I want more Beatles re-mastered like this!
So, if you know that the DVD-A track is higher resolution than the stereo PCM track, but is lower in level...it sounds like you're asking if your volume control will effect the sound adversely? I've compared the DVD-A and DTS 5.1 mixes at home and prefer either to the stereo tracks.
Do you want to know which sounds better? Have you tried it? I wouldn't see an advantage listening to a downmixed 5.1 when there's a stereo PCM track available, though.