Since PSX units are quite rare and I don't own one, it's only possible to discover how Sony marries the HDD units to the PSX itself if someone helps me.
From a boot ROM dump of a DESR-5000 unit I got from AssemblerGames (Sorry, but I honestly can't find that post now D:), it seems like the boot ROM does not have any special HDD modules related to marrying the HDD to the PSX unit. It has newer versions of HDDLOAD and PFLSLOAD than my SCPH-39006 (Probably the same as a SCPH-50000 series), but the ATAD module in it doesn't seem to issue any special commands. :/
From the first 1GB of data dumped and sent to me as a sample, it appears to have been totally obfuscated (Not just XOR'ed, but really brutally mutilated). But why? I think that it's because the PSX's HDD units have a custom firmware that encrypts the data as it gets written onto the HDD unit (By the HDD controller PCB).
But I have no evidence that this is exactly the case, unless someone helps me to prove or disprove this theory.
If the data is protected with such a method, I believe that it's possible to access the data properly using the PSX that the drive was married to (Using the standard ATAD module) and to copy the data out onto another disk to be used with yet another PSX (After patching the files to not require a "genuine' SCE HDD").
The target PSX will have to either have some modified boot files installed into it's flash chip or on a memory card (FMCB style), to facilitate booting onto the non-Sony HDD unit.
Then of course, we have to live with the assumption that the PSX has Magicgate keys like a retail Playstation 2 console, or it will be impossible to create such a patch (Think: TOOL vs retail PS2). -_-"
Is there anyone here who won't mind working slowly with me to try to solve this?
Personally, I don't think that I can go very far due to my lack of resources to make this a really large project with priority, but I would like to try to increase the spread of knowledge and understanding of this rare and unique system.
Basically, you only have to try to get FMCB to boot on your PSX to run the tools I give you. You don't have to remove your HDD unit at all.