> On one hand, understandable; on the other, again, the software is effectively useless because of this.
Just in case you didn't already know, you can use Flatseal[1] to add the symlinked paths outside of those in the default whitelisted paths.
I think it's a good thing Flatpak have followed a security permissions system similar to Android, as I think it's great for security, but I definitely think they need to make this process more integrated and user friendly.