Aranym+FreeMiNT/boostrap+MMU isn't possible.
Brought to you by:
joy
(and has never been). You can boot an MMU build of Aranym + FreeMiNT+MP from a disk image but as soon as you switch the identical builds to the bootstrap mode, it doesn't work. It seems like Aranym forgets to do some initialization because console says "MMU is disabled".
It's up to EmuTOS (operating system), not ARAnyM (hardware), to initialize the MMU. Will be fixed in EmuTOS.