I think for independence from portage autotools-utils.eclass should have its own implementation of econf.
Could you elaborate? Do I understand correctly that you mean inlining the econf code into autotools-utils_src_configure? Why would we need that?
Having an econf implementation in autotools-utils would help to have exactly the same behavior on all package managers. And I would only add the EAPI>=5 econf parts. If we ever default to empty phase functions, it would be bad to still rely on this huge internal piece of code.
I still don't think this will be beneficial to us in any way. And definitely not the way of least surprise. I'm rather working on making autotools-utils use more of standard functions rather than reimplementing them.