Prefabs

Chisel works with Unity prefabs. A prefab can hold brushes, generators and composites, and what it adds or removes is done in the level it is placed in.

A window or door prefab can carry its own hole: a Hierarchical CSG composite with a subtractive brush for the opening and additive brushes for the frame. Drag it onto a wall and the wall gets its hole with the frame in it; move it and the hole moves with it.