You don't have to physically move the NVME or drive from the MacPro5,1 to perform an macOS update.
You can easily do this:
(I) boot to a different drive (or a linux live CD if you do not have a second drive) on the MacPro5,1
(II) on the MacPro5,1's command line, do: dd if=/dev/myharddisk | ssh name@mygentoolinuxserver 'dd of=file.raw'
(III) launch a QEMU macOS instance using that file.raw as hard drive in linux, with a Metal graphics card passthrough to the instance. Then, perform the macOS update within the instance.
(IV) then in the linux host's command line, do "dd if=file.raw | ssh name@mymacpro51 'dd of=/dev/myharddisk && reboot'.
This can all be done on a remote linux server. No need to move any physical thing actually.
Of course, linux distros are more friendly with Mac since they share many Terminal Shell binaries, but also using Windows I was able to create working clones of HFS or APFS Volumes, not only with installing "dd" through windows prompt, but also with some third party partition software.
Windows is becoming more linux friendly too, not by chance I remind that Microsoft acquired Github last year.
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Keeping El Capitan is starting to become useless as it can’t read APFS volumes and you can’t split disks with APFS and HFS which is useful to shorten a disk down for archiving and restoring.
In El Cap a partitioned disk is one big disk. Hybrid disks: with APFS and HFS are treated in Unix as two separate disks which os handy.
If I don't get wrong, booting from a 2010 or later Mac machine with latest HighSierra installation (essentially with APFS firmware enabled), you can boot from an El Capitan USB Installer (10.11.6 BaseSystem.dmg) and it will be able from its (Recovery) DiskUtilty to read the APFS file system, but not write, I guess read-only is suffice to take an image of it.
The same applies to Sierra of course, with advantage that from 10.12.6 (they introduced a beta apfs kext) you can do that also from the normal booting Sierra, and APFS disk will be shown also in Finder. But mounted as read-only, not write, writing directly into APFS Container is only possible from HighSierra.
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