Not sure what you are trying to accomplish in the first post. But what you want is the package manager development tools package. That provides a button to move a package out of the package cache so you can make changes.
For collision filters you can clone the collider as mentioned Modifying PhysicsShape's CollisionFilter at runtime .
And the filters are like they are for performance reasons. And there are probably good solutions for whatever specific challenge you have so I would just post them as you hit them. Physics team is very helpful.