As far as I can tell you won't have the ability to use any of the ARM framework part of MiSTer.
That means you can't switch cores, can't use USB controllers, and miss some utilities to load ROMs that are core-specific.
None of those are really critical for Arcade cores as far as I know.
I think this would be good to use as an "end installation" device
i.e. you put it inside a cab to use regularly, never changing the core (other than upgrades).
I could recommend using the same GPIO pinout as the Pandora's box controllers (perhaps modifying a bit to allow to connect speakers),
so that way you will be able to use this board as replacement PCB for any Pandora's box system (they use VGA internally).
See the pinout diagram here: https://imgur.com/gallery/SF6wTWP