Yes, you can configure out-of-tree, but you can't autoreconf -i -f out-of-tree. I want *zero* files in the source tree that are not meant to be committed. So yes, autotools does support out-of-tree builds, but it still leaves a dirty source tree behind.
Out-of-source *build* is probably bad wording. More precisely, .gitignore should be empty and git status (and the equivalent in the other VCS's) should also be empty starting with no generated files.