hey!
Here is something you could try: install qubes on your normal functioning ssd, then use a disk cloning program like Symantec Ghost to basically clone the ssd with your working Qubes install on it, and saving it onto the M.2 drive. further more, have you tried installing other OS's onto your m.2 drive? Because it could be a problem with the drive itself instead of a software problem. I think this is likely, since it Qubes appears to work normally on a non-M.2 drive (according to you. so the problem should be something drive specific, I think.
i would like to hear from you if it works or not, good luck
best regards, blacklight447
check bios options.
You likely have a marvell based m.2 SSD they have a issue with EFI mode.
I add the following to my xen.cfg to get it to show up.
pci-phantom=00:00,2
This is a know issue with XEN and marvell m.2 SSDs in EFI mode.