Is there a chance there’s some misunderstanding here (and maybe that’s me!)
There’s two aspects in this thread from what I’m seeing. One is that the extensions write their desktop-launch wrapper with a PYTHONPATH set to use the Gnome content snaps. The other is that the during build time, having the Gnome extension defined at all for any singular app forces the PYTHONPATH variable on every single part in the snapcraft.yaml, regardless of whether the part makes use of GTK or Python3 (e.g, it’s breaking Python 2 for me during the buildtime of an Electron app for example).
They’re closely related but distinct IMO, in that it means the presence of the Gnome extensions at build time is breaking certain usages of Python that might be completely obscure to the maintainer. I’m less familiar with the runtime side of things because for me personally, I haven’t seen any regression (but I don’t do much with Python in snaps)
Infact, re-reading the title, it’s not even specifically the python plugin that’s impacted. It’s any plugin that just so happens to use Python (which the python plugin is probably the most common example of 
)