Do flatpaks vs shell see different paths? (eg Pycharm Pro python vs konsole Python)

The solution may in fact be to [use Docker/Podman for the build config]( IDEA-347372 Configure Podman unix socket with Pycharm-Pro on Fedora SilverBlue.)
It turns out that FlatPak is not officially supported by JetBrains:
(Maybe this is the Universe telling me to go back to Emacs.)

Hi, please note that PyCharm is not officially distributed using flatpak, so we can’t assist with this issue. Please consider installing from one of the official distribution channels: