Alright. Before we go any further it would be best to determine what your needs are. So:
1) Did you install Anaconda just to get Python or for the science data set of libraries it provides?
A: For the data science set of libraries. Also, it helps to keep libraries updated.
2) Do you need the system Python you installed for anything that Anaconda does not provide?
A: I don't know if I understood well this question, but I think the answer is no. Anaconda does provide almost all the libraries I need. I just installed a couple more (like talib, tensorflow, keras, psycopg2, etc) and created some libraries of my own.
3) What are you planning to do with plpython3u?
A: I'm planning to create some functions using python language to process data that is stored in real time in the database and then use them as triggers. I would like to be able to import some libraries that I have in python to do it. Some of the functions are fourier and wavelet transforms. If I can't import the library, then I'll have to code the full function, but it's easier (for me) to code them in python language rather than sql language.