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Presumably the attacker would modify the most recent commit which edits the file that they are targeting. It is true that the attack becomes more difficult if you try to target an older commit.

Auditing helps if they try to force push the original repo, but doesn't protect vs someone redistributing malicious clones of the repo.

Reproduceable builds do help, but only for projects that can take advantage of it...

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Every commit references every file. If you change the content of an old commit you would only affect people who check out the old commit. So this is utterly pointless and not what someone would do.

Instead what you would do is attempt to make a file-object that has a certain SHA1 hash identifying it, and a colliding file-object that has the same SHA1 hash. Then you are free to give people who clone the repository different file contents depending on when/who/how someone requests it (if the file content is hosted on github, how to change the file object identified by a given SHA1 hash is an additional hurdle since it's assumed to be immutable and indefinitely cacheable; if you control the host yourself you can just change it whenever you like).

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