In my edperience I had many many problems with OS packages vs pip installed ones. There were really strange dependency issues.
In some cases I encountered dependency hell.
Even if somebody said to me that the core means also using virtualized en I would disagree as places over Internet not always explicitly guide you in that route.
NB. The latest incident was Friday when I've discovered that some CI pipeline ran `setup.py install` that down the lane invoked easy_install, which doesn't have a policy of ignoring bizarre versions s.a. X.Y.Zrc1 or X.Y.Zb2 etc. It ran aground when it was trying to install scikit-learn which wanted NumPy >=X.Y.Z, but it already installed X.Y.Zb1, and it didn't realize that this version should be OK (also, it shouldn't have installed non-release versions anyways).
I run into some kind of packaging or dependency problem for basically every non-trivial project. Hence the many "solutions", but somehow most end up worse than the problems they attempt to solve
Edit: Wow y'all are some sour people for voting down this question. I truly wonder how often people run into this problem compared to just complaining about it.