That's exactly why the did bundle a python installation with it -- so it wont mess or be restricted by your system Python.
Giving those folks the ability to use Macs too is a huge deal (and "just install things yourself" isn't really an option -- it's gotten better, but numpy and scipy have historically been the very devil to manually install on any platform other than Windows).
Very, very glad Anaconda exists.
Because on Linux, installing python with libraries has always been trivially automatic. My windows experiences have always been hunting the net for hopefully compatible installers from 7 different sources and hope it won't mess my python installation... And it always ends up constraining the version I can use.
- Python(x,y) was a step forward but stagnated on python 2.
- Sagemath, which bundles a huge collection of scientific software gave up on installing on Windows. To this day, their answer is a virtualbox linux image. (It's also been a strong reason for developing SageMath Cloud, so people don't need to install Sage at all.)
- Disclaimer: haven't tried Conda.