you'd probably patch them with IDA just like how nopsn patches are done. there's a tutorial to set up the environment on psx place, but it's for nopsn. it should be similar with ps4, but it's not noob friendly.
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btw, iirc, IDA costs money, so most devs use the one that's been hacked. I think it's either version 6 or 7.something.
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I think you'll have to unfself the encrypted files to turn them into elf files to use with IDA, but then you can use batch fself to turn them back into self files. I'm not sure if orbis fixed my bloodborne eboot or if that was the app, but the bloodborne eboot was an fself again once I decrypted the pkg with orbis chk, and just removed the eboot.bin for testing.