The problem that it *causes* is that people think that Sage has somehow managed to install an ancient ipython-5.0.0 in their ~/.sage directory. The user that reported this was indeed having problems because of an out of date ipython thet they had installed with %pip. The python package was installed as a --user package in ~/.sage. That is where the macOS app installs all pip packages, being disallowed from putting them into the app bundle itself because that would break the signature and macOS would then refuse to run the app..
The old version of ipython caused the new app to crash with the rather amazing error message "object of type List is not iterable". When the user removed their ~/.sage directory everything worked as expected. But then, after starting Sage, they checked to see what was actually in the directory, and were alarmed to ",find" that Sage had re-installed ipython-5.0.0.
As I said, this idea confuses users, and understandably so. It was not a great idea. There were so many other, better, ways of naming the directory.
Maybe for the next Sage release I will move the pip packages to ~/Library/SageMath-X.Y. That won't stop Sage from creating ~/.sage/ipython-5.0.0 but it will remove the motivation for users to look in the .sage directory and get confused.
- Marc