So for the benefit of anyone who may come across this later, there's 2 solutions to this problem that have worked for me as suggested by the other posters here:
1. Put the standard or Hybrid HDD into an external enclosure and boot to it over USB3. It works and it's cheap, but it's not elegant.
2. Put in an SSD - There's something up with the Logic board (probably the SATA controller as explained in previous posts). It works with an SSD at full speed apparently flawlessly, but it doesn't like HDD's or Hybrid drives, even if they're OEM. Probably a design flaw.
Details:
I started with an HDD and moved to a Hybrid SSHD that would intermittently slow down to 11 MB/s per Black Magic Disk Speed Test.
After success with an external HDD (as suggested in this thread) I knew the computer wasn't totally borked so I bought a Samsung Evo 850 (not pro) that I knew I could just use in another project if it didn't work in the Mini. I cloned my working HDD to the new SSD and then put it in the external enclosure first, and got like 380 MB/s consistently (after repairing permissions, that part was making things funky, but a permissions repair got it working right).
After that external SSD over USB success, I put the SSD in the Mini where it's supposed to go in the standard slot, and now I've had 480 MB/s read/write for the last 3 days. That's over a 43x increase in speed and usability compared to the 11 MB/s I was getting. There've been no slow downs or beachballs or any of the old behavior. Thanks to the posters who helped, and good luck to anyone else who comes across this problem.
1. Put the standard or Hybrid HDD into an external enclosure and boot to it over USB3. It works and it's cheap, but it's not elegant.
2. Put in an SSD - There's something up with the Logic board (probably the SATA controller as explained in previous posts). It works with an SSD at full speed apparently flawlessly, but it doesn't like HDD's or Hybrid drives, even if they're OEM. Probably a design flaw.
Details:
I started with an HDD and moved to a Hybrid SSHD that would intermittently slow down to 11 MB/s per Black Magic Disk Speed Test.
After success with an external HDD (as suggested in this thread) I knew the computer wasn't totally borked so I bought a Samsung Evo 850 (not pro) that I knew I could just use in another project if it didn't work in the Mini. I cloned my working HDD to the new SSD and then put it in the external enclosure first, and got like 380 MB/s consistently (after repairing permissions, that part was making things funky, but a permissions repair got it working right).
After that external SSD over USB success, I put the SSD in the Mini where it's supposed to go in the standard slot, and now I've had 480 MB/s read/write for the last 3 days. That's over a 43x increase in speed and usability compared to the 11 MB/s I was getting. There've been no slow downs or beachballs or any of the old behavior. Thanks to the posters who helped, and good luck to anyone else who comes across this problem.