The issue is not the mATX form factor ... the issue is the OEM Windows OS is keyed to the current Foxconn motherboard/chipset.
The OP may not legally replace the motherboard and reinstall the OS unless it is a "maintenance replacement" (see the EULA) ... typically, a compatible motherboard/chipset.
If a similar motherboard/chipset is not available for maintenance replacement, he would need to choose a model as close as possible, and likely re-validate his OS over the phone ... i.e., no moving into a 990FX-chipset upgrade with a bunch of improved 'bells and whistles'
He might, however, snag something like the GA-78LMT-USB3 (which is a 760-chipset) BUT it has USB3, and he would be subject to the good graces of MS for validation and activation.