Plugging a SBC card into a Mediator would certainly cause major damages.
The PCI slots can't be active for the Amiga and the PC side at the same time.
I have the same problem with an AtéoBus (which is merely an ISA bus with no DMA support): i would like to put there a Pentium MMX SBC that i have but there would be big conflicts with the Amiga.
These cards can only live with the Amiga in 100% inactive slots, such as the ISA slots of the A2000/A3000/A4000.