1. Enable the loose subc mode using the mode menu or the {m k s} key binding:

This will let you edit subcircuit parts directly. Warning: this is a dangerous editing mode: you may accidentally grab and move or delete parts of footprints.

2. Select the target subcircuit(s), e.g. by click them:

3. Invoke the property editor, e.g. using the {e p} keys. When the properties are presented, select p/padstack/clearance, enter a new value on the bottom right and click apply:

The change is made immediately, and the result should be all padstacks having the same (global) clearance in the selected subcircuits.

The property editor is capable of changing the values by a delta, so it is possible to not unify clearances but increase/decrease them. The property editor can change other object properties as well - the same method can be used to set silk line/arc width, text size, etc in all selected subcircuits.

4. After finishing, it's best to turn off the loose subc mode to avoid accidental editing (same process as in step 1.)