For the Mac Pro 2006/2007, can you explain why the NVMe solutions for 10.11 El Capitan won't work? You have to boot using a different boot loader (
Piker Alpha's). I understand jimj740's NVMeGeneric.kext may have KPs as you've explained elsewhere but I think it worked ok when I built my Hackintosh back then. There's also the patches for Apple's NVMe driver (
Rehabman's repository has a full set of those). If they work at all then they should be mentioned for completeness.
About MacPro3,1 and later, updating the EFI is only required for direct boot support. A third party boot loader (e.g. rEFInd) can be used to boot NVMe/APFS without modifying the ROM.
Socket 3 (Key M) M.2 devices are PCIe devices containing a NVMe or AHCI controller. For MacPro1,1, you would choose AHCI unless you want to go through the hoops of trying NVMe (if those hoops actually make it work). MacPro1,1 is limited to PCIe gen 1 speed ~750 MB.s. You would need a x16 card with a PCIe switch to get the full 3000 MB/s of a single PCIe M.2 drive.
The picture of the PEX is unclear. The second 8 looks different than the first. It could be a 6. If it's an 8, it might mean it has more ports (but Apple doesn't need 24 ports so maybe it has less?) There is a comment on the iFixit teardown page that says the MacPro7,1 uses two x16 upstream links from the PEX, leaving 64 lanes for downstream slots. Has anyone posted an IORegistry dump? That's a topic for a different thread.