Further, the ancient 512MB CF card I usually use in my SIDE2 cart, which prior wasn't even recognized by the loader, now works at least a little bit. The 1088XEL Loader now recognizes the FAT32 and APT partitions, though it doesn't recognize the contents of the FAT partition. However, SDX can read the contents of the APT hard disk partitions, read and write files, etc. In the prior build, SDX didn't recognize that a card was there at all.
I'm surprised that PBI BIOS (i.e. SDX) behaviour has changed at all, although this may be caused by corrections to the device reset code which occurred a while back. The discrepant behaviour between the PBI BIOS and the loader is caused by the fact the PBI BIOS has the ability to mask instability by retrying sector transfers if it detects skipped or repeated reads. I was often tempted to remove that retry logic entirely since it creates the impression that the loader has some issues, when in fact the IO errors in the loader simply signify that the computer cannot reliably communicate with the card. At the end of the day, however, I suppose it's better to have one thing work reliably than neither, although if the PBI BIOS is having to issue retries (which is likely if the loader can't read a partition), it would be worth running RWCRC. The DRQ checks are not guaranteed to catch every transfer error and if the hardware doesn't work 100 per cent reliably in the loader, it's possible that the PBI BIOS will eventually encounter a double read and a skipped read in the same transfer, meaning DRQ will still be deasserted at the correct time despite the fact there's a bogus byte in the sector buffer.
And in the immortal words of Tom Cruise in Jerry Maguire, the 1088XEL has this to say to the new Bios "You complete me".
Concidentally the same film in which he says "Show me the money!".
Thanks all for the positive feedback, and sincerest thanks to Stephen for his kind and quite unexpected donation.