Ok, from what I can tell, the SBI files are not actually patches but they contain subchannel data, which is data on a cdrom that can not normally be read using the normal SCSI commands and can usually not be written either.
They are out of band data which the PSX cdrom drive CAN read and return to the application and such that the game/application have special code, libcrypt, that reads this subchannel from some specific part of the disc and verifies that what the cdrom drive returned matches what libcrypt knows that sony deliberately had written to the subchannel.
Since originally, customer cdrom readers/writers could not read/write the subchannel it meant that if you copied a disk the subchannel on the disc would suddenly be some semi-random garbage and NOT that specific string of bytes that sony wrote in their factory.
Thus libcrypt could detect "this is not a genuine disc", and error out.
Later drives apparently makes it possible to read the subchannel and then if you modify an emulator to take the file containing the subchannel data/the SBI file and ehnance the emulation of the virtual cdrom drive to be "if the games this call to the cdrom drive to ask for data, give the game the content of the SBI file" which results in the game working.
https://documentation.help/ePSXe/subchannelreading.htm
So, I think technically speaking, SBI files are not a patch and they do NOT remove the libcrypt protection code, the SBI files is just a means to "make the emulator return the expected subchannel data when the libcrypt code checks the disk".
I.e. the libcrypt code is still there and operational, it is just with the SBI file the emulator can more accurately emulate the disc content and thus tricking libcrypt to think there is a genuine disk there.
That would not work for EBOOT.PBPs because there is no place in the file to store the subchannel, and the actual emulator itself does not have any means to emulate the subchannel either.
So for this case we would need an actual code patch that modifies the game code and removes the actual libcrypt code/checks from the game itself.
It looks like these types of patches are called PPF patches.
From what I can tell these PPF files are actual code patches that can be patches in either to the ISO itself or into ram by the emulator.
I think a possible solution for EBOOT.PBPs would be to "find the PPF that removes libcrypt for <game-id>", apply the patch to the .bin file, and then recompute all the data checksums that will no longer match as the data has been modified.
These kind of binary PPF patches can probably not only be used to "de-activate the libcrypt code" but also "translate all strings into language xyz" and similar.
Now, to find documentation of the PPF format and to find if there is a repository somewhere where there are PPFs searchable by game-id.../
(I would not care about trainers or similar myself, I think those things ruin the fun of games, but I would like to make it possible to 'rip my game disk into bin/enc' then pop-fe will automatically apply the "deactivate libcrypt" patch so that the resulting EBOOT will work.)
EDIT: oh, where possible, the SBI solution is probably the easiest way to fix this for emulators. It is just a matter of "emulate one more SCSI command for the CDROM drive and have it return the content of the SBI file" and as there seems to be comphrehensive datasets of all SBI files for all games ... so "emualte this SCSI command" and "provide this set of all SBI files" would fix all games in one go.
But unfortunately that is not viable for EBOOT.PBP based game conversions :-(
EDIT2: Turns out I have two games with libcrypt. Need for speed porche 2000 and vagrant story, so now I just need to track down if I can find a PPF file for them and try how this will work.