As of now, I set up lr-mame2003 as I need it with a few options, saved the retroarch.cfg once and turned off "save on exit". It's now pulling the video parameters of every game I throw at it based on what I have listed in the file I posted to you.
i guess i'm not totally clear on what you want to achieve. retropie at the basic level has a global retroarch.cfg (/all/retroarch.cfg) which has the baseline settings for all libretro (lr-) emulators. then beyond that there's per-directory configs (eg /mame-libretro/retroarch.cfg) which by default point to an input_remapping_directory, and then defer back to the global config, as you've shown above.
then additionally you can have per-game overrides, per-core overrides, and gamename.ext.cfg overrides. to set up any of these you don't need to ever set 'save on exit' on. it's probably safest to manually create them, actually.
so i'm not sure exactly what hierarchy of configs you want to end up with, and what you currently have.
Ultimately... to not have this happen the next time I choose to upgrade any core part of the build... LOL. I thought I was doing something good by updating RA from 1.8.8 to 1.9.4 then .5. But my build has apparently become so convoluted that I disrupted areas I wasn't aware of.
I'm going to say by adding in the scriptmodules I added more issues than I was aware of. Just the idea that I turn off a shader and I loose performance means something is crossed somewhere.
I'll keep poking around my config files and hopefully find out what's causing some of this. What you and mitu offered was insightful and helped a lot.. but I think this is something that will ultimately leave me with a "it's working good enough" scenario.