I'll share my nfig and nfig for the baseline XL and my 5200 setup when I have a chance that will illustrate the difference in configs. The setup of the BIOS files appears to be different enough for each system to justify the potential of having to config it through the atari800 menu on a per system basis, but that's MHO.
I didn't see a lot of overlap with maintaining a common config and it seemed far easier to drive everything through the config and runcommand command line parameters. I took the approach of separating the roms, runcommands, and configs for each system. Considering this is currently the only 5200 emulator for Pi, that makes it less of a conflict issue with other emulators. It makes launching into games very seamless however. That essentially means creating custom roms for a specific emulator. a52 data with a cart-type header used by atari800 emulator.
I ultimately ended up using the Cart guide to create. The 5200 comes in 4k, 8k, two version of 16k, and 32k cart types, and it must be specified on a per ROM basis. Specifying a cart-type in the command line is essentially pointless. That lead me to the conclusion of maintaining separate configs for each system and referencing them using the -config parameter. I've essentially been using the emulator strictly for 5200 emulation, but everything I've read gives me the impression that the config needs to vary quite a bit depending on the system and not much is shared in common.