Not likely. Such programs want direct or at least quite low level access to the drive to push the geometry beyond spec. I'm unaware of methods to directly loop a floppy drive into the AO486 as if it were physically attached to a simulated controller. As far as I know, AO486 pushes and pulls sectors from MiSTer Main and the abstraction of the drive sits there. It might be possible to use /dev/fd0 as a backing store for just a bunch of sectors, but DOS on the FPGA will never be able to address the real tracks/sectors on the drive because of the abstraction.