As far as the Python question… we build our binaries on the GitHub infrastructure. Since these build servers contain multiple versions of Python, this is the path on the build server. (And thus the fallback comment.) It will go away if you set a path to python in Avogadro:
Extensions => Set Python Path…
As to Wayland … this is a known bug: Will Avogadro support Wayland?
We should be able to switch away to a different OpenGL library in the next release.