Great to hear you're investing time into improving the texturing! I know what the problem is with the roof textures, I just don't have an easy solution...
I had introduced the -A option mainly for debugging when I was coding the texture atlas -- and back then, it's been very useful. I agree that it's not as important for most end-users, but I can still see a number of use cases where you'll want to re-create the texture atlas often: if you're
1. improving textures, for example by adjusting contrast, or trying different mipmap options -- I have done this a lot when I was creating the VHXX custom scenery
2. working on lightmaps (and I've got alpha code sitting around [mk_lightmap.py] that aims at automatically creating lightmaps from textures).
Plus, I don't see -A creating too much bloat, so I'd really like to keep -A.
Also (you're probably aware of this): changing the way the texture meta info is stored will break texGUI.py. I agree it may be more convenient to have it in csv for filtering etc. But then, storing all in one file (is that what you're planning?) will make it less convenient to copy textures between regional definitions. Maybe that is something we could discuss on skype sometime...