My counter argument is that we want to expand Sage's user base beyond a small core of researchers, and improve its usability as a Mathematica replacement for students and some scientists who are less interested in things like bleeding edge combinatorics research (they might be but not necessarily the majority). As a Mathematica replacement Sage isn't there yet, but it's good to get a head start on making easier to package and install, as part of that effort. Like for me, if it can solve some differential equations for me and do some integrals I don't care if the version I got through apt is a couple years old.
As for the upstream issues part of the problem there is that some of the upstream dependencies of Sage refuse to accept patches needed for them to integrate with Sage. That's a long story. I think the best approach there, which has already been tried in past approaches to patching for Debian, is to maintain Sage-specific forks of that software that include the necessary patches (IMO they should also be swappable with the originals via update-alternatives if possible). As far as I know there's nothingf legally preventing that, but more the effort involved in maintaining a fork and a package for that fork.
In the long term, I think, it would make sense to completely replace and rewrite some of the code that these external dependencies are used for. But in many cases there's an enormous amount of work involved, and that would only be possible with significant funding. And quite possibly not worth the effort compared to other ways that effort could be spent.
