In principle, the MEGA65 will be able to run any C64 or C65 ROM. So if you own JiffyDOS ROMs, they should work. However, this will not make any difference to the internal drive, except to disable it, since you would need a C65-version of JiffyDOS to have it not clobber the routines that talk to the internal drive.
We do have plans to make a better C65 ROM with much faster speeds on the internal drive, and that would be backward compatible with existing C65s. It seems it should be possible to increase the internal drive speed from ~1KB/sec to 10 - 30KB/sec.