Altium: Query to target Vias in Pads
I can think of two ways:

Method 1

This method assumes that the vias are created as part of the component, and not placed on the pcb directly.


Select all components [IsComponent] and move them away, dragging their attached vias (primitives) with them.
Select remaining regular vias with the mouse and somehow mark them, in this example by locking them.
Move back all components.
Filter using [IsVia and Not Locked]


Method 2

Give the via some property that will make them easy to filter out.  For example, make all diameters of via in pads odd numbers that are very close to your desired drills, like 0.099mm instead of 0.1mm.  That way you can filter by drill diameter (or some other attribute).