Reading the description of the archive.org project at https://archive.org/details/apple_ii_library_4am&tab=about makes it clear that this effort intentionally deconstructs and documents the original copy protection.
Other than as an exploration of copy protection, though, I can't help but wonder if the simplest approach to preserve and run the same software today would involve an appropriate emulator, more accurate floppy drive emulation, and the unmodified original disk image. The crazy amount of self-decryption and obfuscated code wouldn't matter as long as it found what it expected on the disk; the modifications just let it run on real hardware using a copied disk.
Apart from allowing the use of the original unmodified disk, emulation would also avoid the possibility of missing more subtle copy protection schemes. This particular disk made things easier by just stopping the game at the start. Some of the worse copy protection mechanisms developed later would detect a copied game, leave it somewhat playable, but make it either exceptionally difficult or intentionally broken near the end. Sometimes they would include a more obvious copy protection scheme to defeat that prevented playing the game at all, so that a prospective cracker would think themselves successful once the game starts. See http://media.earthboundcentral.com/2011/05/earthbounds-copy-... for an example.