How to apply a rule to only one component in altium?
As this problem regards with the footprint itself, instead of being a problem of a whole net or component, you can proceed making a rule just for the footprint.

I've done this with success:


Design > Rules > Clearance > New Rule
Change the new rule priority to the highest, or if you have plenty rules, arrange it correctly to make it work.
Enter the new rule properties with double click
In "Where The First Object Matches", select "Custom Query"
Write "HasFootprint('NameOfYourFootprint')
Set the desired values in the Constraints tab, then accept.


Now we are going to re run the design rule checker.


Tools > Reset Error Markers
Tools > Design Rule Checker > Run Design Rule Check


Hope this works for you too.