After an evening of pondering this, I have figured out what I did to screw it up. I have created multiple images of RetroPie setups that were reasonably customized and saved piles of things I referred to as "Clean" associated with those. (For example, known good ROMS, BIOS, and Meta Data like Scraper results.)
What happened was that I missed a step trying to recreate my steps. So here's the abbreviated version of what I did that messed it up.
Wrote the correct, unaltered, unupdated 4.5.1 image to the SD card (I really couldn't believe I would have written the wrong image).
Copied vast amounts of "Clean" altered configs (for a setup that was designed for SNES controller compatibility, and thus didn't use PSX).
Boomie. (At this point, I believe my copying of configs was all it took to scramble it up.)
It should have been obvious when the pixel art launch screens came up (part of the config I just copied), but I honestly recall thinking "Oh cool, 4.5.1 uses the same pixel art things I liked for launching games."
Thus, to your point, I had 4.5.1, with a bunch of 4.4 config wedged in manually after the fact. Worse, because my previously configured system never used PSX (not enough RasPi power when I created it, and not enough buttons when using SNES controllers), I had no idea that there might have been a bug with it that had been hiding in what I was copying.