Only applies for the Stalker levels. PrCs thus far don't care how you entered the class. I'll note the wording on Mage Hunter:

At every even-numbered level, a mage hunter gains new maneuvers known from the Scarlet Throne, Steel Serpent, Solar Wind, and Veiled Moon disciplines. He must meet a maneuver's prerequisites to learn it. He adds his full mage hunter levels to his initiator level to determine his total initiator level and his highest-level maneuvers known.