If "disc archives" contains subchannel data in separate from disc images section (based on dev wiki page), and Sony emulators using them, then it means psxtract ignoring this during decryption and extraction. From this came wrong assumption that those emulators patching stuff on the fly. :/
From the 3 posible ways we was speculating most probably is going to be needed to update some tools, after all the hack used to run PS1 and PS2 classics in PKG format has been always about trying to copy the official structures in the best way posible because are running with official functions
The good one
The concept is simple, the subchannel data needs to be packed together with the disc image (every disc have his own)
Some days ago when i was learning about all this i had a tendence to think that the most probables was the others, mostly because ive heard many times before that sony was defeating his own libcrypt protection by applying patches in the disc image in the official PS1 classics, and is the kind of history that is catchy because is a bit laughable

I mean... if sony was using "dirty" hacks it would mean the emulator doesnt supports subchannel data at all... so implementing it would be a completly different story and something very tricky theoretically
libcrypt patches hardcoded inside the emu
This was my second way of thinking, just because is easy and i was still considering the emulator doesnt support subchannel data... in other words still a "dirty" hack but a bit more handy to deal with it, more time costly and prone to human errors because it would be needed to check and debug every patched area individually, this is also why i was wondering if the emulator could include the complete collection for the 229 discs... lot of work, but is the kind of thing after it done it becomes "legacy" (not needed to touch it ever with a 10 feet pole, 100% working)
And it would be like the kind of area inside the emu .elf that most of the people reverse enginerring the PS1 emulators was labeling as "unknown clusterfuck of data", you know... completly unknown and zero hopes to identify it... so forget about it and better spend the time in something more interesting
subchannel data hardcoded inside the emu
Pretty much like the previous, it would be another clusterfuck inside the emu .elf but this is way easyer to do, can be automatized and is failproof... is just... it would imply the emulator supports the subchannel and in that case it seems they prefered to pack the subchannel data with the disc image
Btw, in the PS2 emulators they was doing this with the game configs, is not so crazy for other tools, the concept is we create a clusterfuck with the data for the 229 games (1 file instead of 229) like if it was some kind of database where can be applyed other features (to prevent duplicated entries, compression, to give them a different ID, whatever) and then that database is shipped with the tool, basically is like doing a .zip with all the files and preparing some functions to access the .zip content (but im not telling it only for the compression, the configs in the PS2 emulators are not compressed but the way how they reduced size is nice stuff)
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Anyway, this feature is nice for PS1 classics in PKG format/HEN, and some PS3 backup mamagers that could do the conversions in betwen encrypted/decrypted disc images, and the swaptrick with the placeholder
But for CFW where is used the standard disc image is going to be needed to implement new checks in cobra/mamba to deal with the new structure and send the correct info to the emu
So the PPF patches are still handy in the meantime because we are sure are going to work in all cases (ironically are the most compatibles in between platforms/emus), so the list of PPF patches i made in wiki will be useful after all, in the last days when i was trying to figure what to do with the list i changed my mind many times and i was not so sure

Now my tasks in that wiki page are increasing, displaying the PPF patches was a good idea, but if the last specualtions are confirmed and that "garbage" found by devildwarf is subchannel data we can display it in the wiki page too (and this will be legacy, kind of thing that could take some work to complete, but is not needed to modify it ever again)
The PPF patches on the otherside... i want the page to be like the others for PS2 configs, with some people publishing "partial fix" and later some other replacing it by "version 2" and so on until we reach a point where we get the "holy grail LC.ppf" for every disc, lol