Well, this was unexpected. I found a configuration that does not cause IDE data corruption.
This is it:
What this is, is a SATA drive connected through SATA->IDE adapter. I have no idea why this works (using the same cable too) but the CF Cards do not work on my system.
I can copy files back and forth, boot, read them just fine, no corruption at all. Huh.
What speed does this achieve, you may ask?
This is with CPU FASTROM option active. Much slower without it.
So I guess there is a bug somewhere in the IDE code.