Oh, the user above was mentioning slack, sorry.
Pycham is also proprietary. This is an unofficial repackage of the app done by volunteers.
It probably works fine just not for your workload. But I can imagine why someone would want to sandbox Pycharm...
And to your issues, have you even tried to poke holes in the sandbox? You can use KDEs settings or Flatseal.
Launching a terminal can be done via flatpak-spawn.
I think you dont get this. Flatpak is important. Linux is completely powerless, there are people installing invasive apps which then can do what they can on Windows. Compare that to Android (which is obviously way less complicated because of how apps are used).
Flatpak is a new system to build apps, of course it cant read some ~/.config directory thats the point. If you store stuff there you are used to a different way and will need to adapt. Or you use their official binaries.
Just because apps are not ready this doesnt mean it is not clearly the way we will do GUI apps. 800+ apps officially verified. We are approaching official universal Linux support here!