Yes, the Hotkey + B method does work.
What I was hoping for is that there was a way to hint the proper behavior that would be easier to maintain for people with large collections.
The two ways that I can think of would be:
1) Have a psxanalog folder that turns on analog controls for any game in there. (similar to how gb2players exists)
2) Have the rom names note if they are analog. (similar to how 5.11 added support for hinting wiimotes)
Maybe this would be a good starter project for trying to add an enhancement to batocera? I would guess number 2 would be easier to implement, but I'm not sure.
I think I'm interested enough to try though.