I would only commit into revision control what is called in GPL v3 legalese the corresponding source, and try and get it as small as possible. I never commit configure
et al. when I can.
Portability isn't really the issue, since the autotools are meant to assist portability. At any rate, you can always blow away autotools generated files like configure
and replace them with ones that work for you. The issue is that (when comitted) these files will have a strong tendency to become conflicted and otherwise show change activity when nothing has really changed.