I think for people who are already using DarkSoft zipped ROMs, it's no big deal; or it's something they've already dealt with.
It was jarring for me because I forgot all about that option for the Neo Geo core. I had just been using .neo ROM files.
You can (obviously) do whatever you want with your time, but I think it would be a waste to put too much energy into the ROM names (because of what I stated above).
I also think too much time has passed since the introduction of the Neo Geo core, and it was really up to furrtek to choose something better than he did with the names (I'm not complaining, the guy is awesome). That's if there's even a better a option available. At this point, you are just working with what's available.
So just to clarify, using update_all after 'installing' the RBF/MRA files - those ROMs will not work. But if I zip the ones I have currently (Darksoft) for the "console" version of the Neo, those should work. Am I understanding that correct?
edit: Yep! I was correct. Just tried it with the Darksoft set and it works just fine.