An update on this: I uninstalled the secondary SSD (970 Evo Plus), so I now only have one SSD in the system (the 980 Pro), and now my 3DMark PCIe benchmark scores are back to normal, or close: 22.3GB/s, just a bit lower than my previous record of 23.5GB/s (this may be within margin of error, I don't think this particular benchmark is extremely precise). So the problem for that was just PCIe lane allocation; it persisted even after I disabled the secondary SSD in Windows's device manager, it seems the soft-disable is not good enough you really have to yank the thing out of the M.2 slot in order to free its use of PCIe resources.
But my Magician benchmark scores are unchanged, 160K random write. Still waiting from some good soul at Microsoft, Samsung or AMD to release a fix for whatever causes this.