The problem I have with apt, yum, etc... is that the packages for development are so old that you're going to be compiling from source and managing your own updates, which is exactly the problem a good package manager should solve.
The big difference is that packages that land in the official apt repositories have been heavily tested by the apt repository maintainers. Anyone can push a package to PyPI for example. There is a clear trade off between using packages from apt/yum and your toolchain's package managers.
In practice, I do find it much easier to pin dependencies and install from my toolchain's package manager (pip/PyPI).
