I had the same issue and I believe there is not a solution currently.
I asked the following question to Altium's Tech Support:
"I am attempting to create a PCB library document (a footprint) with a via that does not simply extend between the top and bottom layers. While I can modify the Layer Stack Manager (Tools -> Layer Stack Manager) in the PCB Library Doc environment, when I click on the "Drill Pairs" option everything is grayed out. In other words, I can't seem to include a via with my component unless the via goes through all layers. Is this an option? Am I doing anything wrong?"
Their response was:
"Unfortunately, it is not an option to add Drill Pairs to the library. This is a legacy tool that was intended to be removed. I apologize for the inconvenience. You would need to create the drill pairs on the PCBDoc itself."