His powers are clearly strong, as even Scully didn’t realize that she was speaking to her son rather than a random man (played by Francois Chau of Lost) at a gas station until she and Mulder checked surveillance tapes.
Despite multiple opportunities in “Ghouli” to turn to Mulder and Scully for assistance, the teen decided to keep to himself.
Jackson/William had to fake his own death in order to escape the same fate as the Van De Kamps.
However his powers work, they don’t change surveillance footage, and the dynamic duo saw enough to know that their biological son is still alive.