Base coordinate points problem :/

Good to know! I have found that the easiest way for me to run clash detection with a linked model is by using the Bimorph package. There is a node inside the package that pulls the linked elements in their HOST location (meaning where they currently are in the model). Most of the OOTB nodes pull the location of linked elements from where they are in the LINKED model. (Which, if I understand your problem correctly, is what is going on with your model.)

What I would recommend is looking at Thomas Mahon’s post from my previous link and he explains in detail how to correct your problem.