GNU Autoconf is just GPL (a combination of GPL-2.0 and GPL-3.0, it looks like -- probably on a file-by-file basis for historical reasons).  There is a v3 exception that allows certain outputs (derivatives, as far as copyright law is concerned) to be distributed under other licenses, including proprietary licenses, but that doesn't make GNU Autoconf itself either non-free or non-open-source.  It just weakens its copyleft-ness a bit, but copyleft-ness is not required for FOSS.

Regarding tivo-ization, that's not an FSD-vs-OSD difference and it doesn't affect the covered licenses.  It's just a difference of interpretation, one that could be applied equally well to either the FSD or OSD.  The OSI's answer to the second point has always been that it's the license that's applied *to the source code* that matters.  In other words, it's not even meaningful to say that a binary is "free software" or "open source" in the absence of source code anyway, and if you do have the source code than *that's* the thing whose distribution under the license matters.

For the record, this is what happens every time I try to get a concrete example of any actual difference between "free software" and "open source software": it turns out it's either not a difference at all or it's a difference of interpretation that depends on the party doing the interpretation (i.e., not on the FSD or OSD itself).  In other words, the FSF interpreting the OSD would come to the same conclusion (in these situations) that they come to with the FSD, and the OSI interpreting the FSD would come to the same conclusion they come to with the OSD.

In more than 20 years, no has has yet shown me a license whose terms clearly match one definition but not the other.  I am fairly sure that no such license *can* logically exist, even in principle, and my attempts to find a disproof of this belief have thus far failed.