For the first one I don't have a clue. The second, if the objects that are removed are hardcoded (or loaded from config at startup) you can simply skip the clipping for those objects and thirdly clip the custom ones as you would with other objects with the same system.
Looking at the code though it's probably easier to just rip the whole clipping system out and replace it. I've written a full clipping system with just these resources:
Path Finding – Coke And Code
https://www.rune-server.org/runescap...lculation.html
and the CollisionMap.java and MapRegion.java files from Majors 317 release:
https://www.rune-server.org/runescap...17-client.html
If you set your system up like this it's 100x easier to remove/add objects (and their clipping) and it also helps if you ever want to work with map palettes.