The front inserts (pre '89) or struts ('89 on) from koni do not come with the top caps and you have to re use your old ones.
You say the bonrath ones are lowered, how are they lowered ?
I am guessing the external part of the spring sit is bent further compared to standard so the spring sits higher when on the car which in turn raises the spring position and will lower the car.
Maybe try and get hold of standard set of spring seats from a breakers and try them out.
Also did you refit your old top mounts as it may be these that have given up and are creaking rather than your spring seats?