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.
My total nightmare experience has been with CMake, with a project that mixed C and C++. IIRC it had to do with trying to get something to work on LLVM / macOS which it wasn't originally supported for.
(FD: CMake developer) I certainly understand a lot of the gripes that people have had, but the amount of tribal knowledge for obscure platform behaviors encoded in CMake is…vast. I am certainly in the "things need to improve" camp, but I don't think burning all the bridges that have been built is the way to go either.
The idea with autotools is that the generated configure script (and other assorted files) is supposed to be forwards and backwards compatible with different systems. It's not perfect, but the behaviour is mostly locked down at the time it is built, based on the particular set of macros it is generated with.
There are definitely aspects of this which don't work (it's nearly impossible to test, getting specific versions of autotools is presumably a PITA, and the make-in-bash-in-m4 language is deeply cursed), but the overall design does make some things better.
For example, if your project needs a specific version of cmake, your users will have to figure out how to install it, but if your project requires a specific version of autotools, only your developers need to install it.
(FWIW autotools is on my 'never again' list of technologies; it's incredibly cursed)