I would stick with usb, i mean you could clone the setup up settings, so if you pull you hdd it will boot the same but use the space of the boot drive, but to me its just wasted space.
What im going to do it have Coin Opps Arcadia 6 And Next r8 running from the internal drive, and Bt install from Thumbdrive that way the best of both worlds. As all it does is create a Dir structure on the drive.
I think my unit has a NVME port to, would be nice fast boot.