I think that's backwards. The developers of unix packaging systems (the Debian packagers in particular) misunderstood the roles of these languages. Writing unix-like tools is a small niche, Python is exceedingly useful outside that niche, and Python 3 is necessary for a lot of very useful things that developers build. Java has been extraordinarily successful despite having hardly any system tools written in it, and I think part of that's the sheer good luck (due to accidents of licensing history) of the likes of Debian not trying to integrate Java deeply into their OS; Python and Perl would be much better off had the same approach been followed.
I think I was unclear about my main point. Python and Perl have many applications outside Unix tooling, but then again so does C. Both sort of started out as "better shell script," and both were seen as such, but they were also seen as stable foundations for serious, long-lived software.
You can build stuff on top of C, Fortran, POSIX, etc. in 2016, and be pretty confident that it will still work with their 2026 versions. That's not valuable if your slapping together an MVP that no one will care about and will die in a few months, but it's incredibly valuable for developing big, complicated software. Or for little personal utilities you want to write once, then not have to maintain. Perl and Python moved away from that longevity, each in its own way. Maybe that will make them better suited to a world of continuous Cloud-based churn, but there's more to life than that.
I find the conservatism of C, Fortran and POSIX has made them almost useless for developing big, complicated software. Compatibility is important but so is evolution. Certainly I think the deprecation cycle for Python is not overly short.
