@rridenour Once you get a better feel for the way each version of MAME relies upon a corresponding (and different) romset, you may reconsider using the Arcade folder. As you figured out, it isn't very useful when you drop an entire romset into the folder if you want to leverage multiple versions of MAME. You will inevitably run into conflicts. Where Arcade DOES make a difference is in "uniting" the interface for arcade games. In other words, non-technical users understand what an arcade game is, but may not understand the differences between AdvanceMAME, libretro cores, FBA, and so on, nor the technical reasons behind using one version of MAME for one game and another version of MAME for another. By combining ROMs under a single folder, you effectively strip the interface down to a single decision for the user: Arcade, and you manage the emulators that get used per ROM with RunCommand settings.
This idea, of course, requires a fair amount of "rom management" to keep everything straight. Instead of dropping the entire set into Arcade which would overwrite ROMs from another set that are already there, you have to mix and match individual ROMs and track which emulators you are using to launch them. This probably means you are storing the entire sets off-system and keeping track of what you use to launch each game in a spreadsheet. It seems like a lot of work, but for me, it's worth it for how it simplifies the interface. I am all for having options, but I love that I can present a clean, intuitive interface to users who don't understand (and don't want to understand) what is going on under the hood.