The major downside of using git clone build workflows from an autotools project is that your build environment and the developer's may have different enough versions of autotools that macro incompatibility introduces more problems for you to solve. I've noticed this less recently (say 5 years) but still has come up occasionally. While a distributed tarball will have the "developer blessed" autoreconf run and declared good by way of releasing the tarball.

Without that process the options are committing generated files (boo) and burdening those that would build from a git clone instead of a distribution tarball with the demands of details from the development environment. That's intentionally a little vague because of the variety of things that can ultimately affect the autotools output.

All of this is kind of the design of the autotools build process and could very well be a reason to take a harder look at it and the tradeoffs incumbent on its use.