The points from an external merge can not be used as reference to create point patterns and holes.
The pattern only allows the selection of sketched points and datum points features created in the same model. It could exists a third option that allows selection of points regardless what kind of feature is, including those coming from the external merge. Regarding the hole feature, the software does not allow the selection of datum points from external merge as a hole center.
These two restrictions limit the functionality to use models as reference to control geometries in other parts without referencing the assembly. As work around, it is necessary recreate all points referenced on the merged points to be able to use as reference for a pattern.
We have additional work if we add or delete points in the merged part. In parts which depend from amodel, it is necessary redefine all the parts to create the new or delete the old references.