I know the plan is to switch to a doc makefile, but the issue would be the same.

Calling os.system("sphinx-build ...") (or directly sphinx-build in the Makefile) will pick up a sphinx install outside of the current environment, which may or may not have an unrelated (e.g., older) version of matplotlib installed. Instead, the command should be something like python -msphinx build ... if sphinx offers that option, or we should use a wrapper script otherwise that makes sure that sphinx is used from the current environment only.