I have a 2012 Mac Mini with a working High Sierra install on a SSD (APFS Volume) in an USB3 external enclosure mounted on
/dev/disk2s1 according to Disk Utility
After I moved that same SSD to the internal SATA HD slot, it no longer appears as a boot drive. Disk Utility would still recognize the SSD on
/dev/disk3s1 as a SATA drive. Also tried resetting the
NVRAM but that did not solve the problem.
I moved the SSD back to USB3 and everything still works fine.
I backed up my data with the SSD connected by USB3 and then tried a time machine recovery to the SSD installed as SATA. Also tried a fresh install to the SSD after erasing the partition. After both efforts, the SSD still will not appear as a boot drive when I hold the option key on startup.