Hi,
The best way is to create a hole in the correct positon in one part, then go to the assembly. Activate the mating part, and make the hole on the correct face, and use co-axial for the reference, as opposed to linear - it's in the Placement menu in the dashboard.

Intralink references independent geometry from other parts. It shows that independent referenced part is a ghost object, but when you check the assembly in, it breaks the dependence between the origin of references and the copied references part.