Correct me if I'm wrong (please, I'm considering using something similar in a project), but RetroAchievements requires Retroarch, which is GPL v3, on non-Windows platforms. Which means if they use it they have to leave the hardware open so that end-users can load their own customized copy of Retroarch onto the system. Now that shouldn't be a problem normally, but if they're locking down the system because they're serious about enforcing the encrypted ROM backups and store downloads, then that's going to be incompatible with GPL v3.
Otherwise I totally get where you're coming from, I've seen a ton of people and companies confuse GPL with non-commercial usage. But I get the feeling in this case they really can't, unless they're willing to back down on enforcing encrypted ROMs. I'm ignoring the liklihood that it'll get hacked anyway, that doesn't make it GPL v3 compliant afaik. I'd guess it's one of the reasons they're going with Mednafen, since it tends (depending on the core iirc) to be GPL v2 which is more permissive on closed systems.