Thanks for posting the system check output.

On a preliminary sidenote, the "Please Fix" section suggests doing something like copy+pasting the following:

echo "" >> ~/.cshrc
echo "setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace" >> ~/.cshrc

... which should be totally unrelated to the present Python question.

Back to the Python stuff:
How do you start a conda environment in your normal shell usage? I think the problem lies with your matlab-called zsh doesn't appear to have your conda environment started up.

Also, I would assume it would be easier to have the AFNI binaries added to your path from the shell setup (outside matlab), then to try to add/append path things in Matlab. But, based on your afni_system_check.py output, I guess that is the case? (Did you run that system_check from your matlab env, or from the terminal command line itself?)

--pt