When you follow the official pymol guide to locally install the script repository: https://pymolwiki.org/index.php/Git_install_scripts the mtsslPlotter.py module fails to initialize when no matplotlib module is found. Emerging dev-python/matplotlib solves this. Would it be possible, maybe, to install matplotlib through a USE flag for pymol?
Pymol itself doenst depend on this package. Its dependency of some external scripts. So its up to user to install needed dependency