Sorry for bringing up an old thread, but I spent a good number of days really investigating if this was possible since mSATA & mPCIE actually are almost pin-for-pin compatible, and I thought it should actually be possible in theory.
Most of the PCIe signals are not connected in the mSATA standard, and the pins that had 5V applied were also not connected (on my particular SSD).
I got as far as creating a modified devicetree that activated the SATA protocol and set the mux such that it would be routed to the mPCIE connector, and turn on the voltage regulator to supply power to the SSD without enabling PCIe.
Ultimately it didn’t work because annoyingly whoever designed the mSATA protocol made one key difference - they swapped the polarity of the SATA
B data pair (aka.
PERn0/PERp0)!!! Argh. It would have worked if the polarity matched PCIe.
Anyway I think this should settle it for sure that you can’t pop an mSATA into the on-board slot.