It depends on the extent to which the git repo is s product for end users vs. for developers. Traditionally, the product for end users was the source tarball... but also, traditionally, we didn't have git. :)
The whole point of autotools is that the output (./configure) is highly portable and can be run on basically any mostly-POSIX-compliant /bin/sh. You don't need to install anything beyond sh and make just to perform the build - compare with a design like Bazel where you need a piece of software to do the build.
If the generated files change rarely, checking in and committing the generated files means people who are just making code changes (or no changes at all) don't need to install autotools.
Also, there are functionality changes in certain versions of autotools; you might want to make sure your users get a feature that was implemented in a recent version of autotools, but support users who are running on an older OS that doesn't have that version packaged.
(If you expect the git repo to be primarily used by developers / contributors instead of end users who are just building it, then you should definitely gitgnore the generated files, but also make sure to include them in the release tarballs. "make dist" will do it. You should also guide end users to download that release tarball instead of an auto-generated tarball of your git sources - GitHub and GitLab both have support for file attachments in their release feature, these days.)
In our modern world, this might be less important because installing software (even specific versions of software) is a lot easier. But then our modern world probably deserves something other than autotools, because a lot of what makes autotools hard to work with is the fact that it's intended to translate down to sh/make. (Options I'm aware of that look fairly reasonable include Meson/Ninja, CMake, and I guess Bazel.)