Hi Sjoerd,
The CLI uses the Python interpreter that is found first in the PATH variable. In your case this interpreter is the one that came with ArcGIS. I can imagine that this is a non-standard version of Python to be able to work with ArcGIS. Miniconda is a Python distribution by a third-party, Anaconda, that uses Conda as a package management system. Although using this with the CLI might work, we do not actively support using Python that comes with the Anaconda/Miniconda distribution.
VIKTOR just uses plain Python and pip (the preferred package installer for Python). If you use viktor-cli install a virtual environment is created with all the packages you defined in requirements.txt by doing a pip install. You do not need to activate this environment yourself, this is handled by the CLI