Ah, I didn’t know it was on PCI. I assume it was a grown-up HCI that could do bus arbitration and mastering on its own. I’d agree with your general guesses, then.
See stat_crabhead’s posts starting around Question about sd-card speed - #8 by Stat_headcrabed The higher clock rates on that chip are only available at 1.8V and they nailed it to the 3.3V rails and it’s shared with several other chips. You can’t just trivially cut that pin loose and re-anchor it and then remove the software lock on setting the clock speed to “fast”.
Hardware limitation or hardware bug? Tough to say, but it’s pretty likely to get picked up if they ever decide to lay the board out again for a respin.
SD being awful is one reason so many people were so anxious to go to PCIe…before discovering IT was disappointing, but at least faster than SD.