I would go further than that: all files which are in a distributed tarball, but not on the corresponding git repository, should be treated as suspect.
Distributing these generated autotools files is a relic of times when it could not be expected that the target machine would have all the necessary development environment pieces. Nowadays, we should be able to assume that whoever wants to compile the code can also run autoconf/automake/etc to generate the build scripts from their sources.
And other than the autotools output, and perhaps a couple of other tarball build artifacts (like cargo simplifying the Cargo.toml file), there should be no difference between what is distributed and what is on the repository. I recall reading about some project to find the corresponding commit for all Rust crates and compare it with the published crate, though I can't find it right now; I don't know whether there's something similar being done for other ecosystems.
Yes, it sucks to add yet another wrapper but that’s what you get for choosing non backwards compatible tools in the first place. In combination with projects that don’t keep up to date on supporting later versions.
A git hash means nothing without the repository it came from, so you'd need to distribute both. A tarball is a self-contained artifact. If I store a tarball in a CD-ROM, and look at it twenty years later, it will still have the same complete code; if I store a git hash in a CD-ROM, without storing a copy of the repository together with it, twenty years later there's a good chance that the repository is no longer available.
We could distribute the git hash together with a shallow copy of the repository (we don't actually need the history as long as the commit with its trees and blobs is there), but that's just reinventing a tarball with more steps.
(Setting aside that currently git hashes use SHA-1, which is not considered strong enough.)
This and the automated A/B / diff to check the tarball against the repo, flag if mismatched.
