How are you adding them to the shell env? If you don’t use python.withPackages they will not end up in the site-packages of the same python instance and therefore not be able to see each other. I gave a more detailed explanation on the topic here the other day, don’t feel like repeating myself this time: NixOS + IntelliJ + Python
I should really start a blog.
If mdformat’s plugin system works anything like the plugin systems I’m used to, that should fix the problem, assuming you use mdformat via a python script and not as a binary?