[speleding]

Perhaps you (or Apple) would still be able to achieve the checksum feature by a smart choice of encryption algorithm?

APFS has file level encryption, so you would in theory be able to detect a flip by selecting an encryption algorithm that gives error upon decrypting modified data. I could see this being worked into apps_fsck at some point.

A similar case could be made for adding it into the compression algorithm, which the OP thinks will be coming to APFS later, popular algorithms such as deflate already have this built in.

[ksec]

Same thoughts here as well, but how does encryption correct data?

[speleding]

Correcting data is much harder, and would require a significant amount of additional storage to provide enough redundancy to be able to deduce the original data. But detecting is good enough for many uses, you would be able to restore the files from the Time Machine before those get silently corrupted as well.