Think of it this way:
Pilot X has the pilot ability : Once per round when you receive a stress token you may immediately discard it.
Pilot X has an EPT, he takes Push the Limit. He can PtL without ever paying its stress cost.
This is not breaking the rules because you are paying extra points for the ability to have him ignore stress.
With huge ships there is a built in cost to every huge ship that allows them to negate all stress received.