I'm talking about cloning the program's git repo and working with that.
GNU programs don't include the generated configure script in their repos; you have to boostrap that first, and you need all the AutoCruft, in the correct versions which that git baseline of the program wants.
It's completely insane. It should be that to create a release of gnu-whatever-1.2.3 you just create a tarball directly out of git using the 1.2.3 version tag. That is the release. But that's not how it works; a release that doesn't require AutoTools has to be specially prepared.
Sometimes I have cheated to build a GNU program from sources. I would find the closest matching release tarball and unpack it over the cloned git repo, then run ./configure and all that. Carefully git-reset any differences and so on.