I see. I don't understand how to provide a coma at the end of the print statement. It can be done in Python2 with a future import making that line a bit awkard to type. Thanks though, this clears up the mystery. I believed .strip() would have taken care of that "\n".
Code:
$ python -c "from __future__ import print_function; print('user@example.com\00user@example.com\00test', end='')" | base64
dXNlckBleGFtcGxlLmNvbQB1c2VyQGV4YW1wbGUuY29tAHRlc3Q=
TIL: python -m pydoc foo and why so many base64 encoded strings end in ==