I don't think it's a plothole. He said no one had given him official permission, just said 'you'll need to go to Ares 4'.
And while he's driving there, he did mention the space pirate thing to NASA, which led to Victor having his 'strange minds think alike' moment. And then they tell Mark about the modifications he'll have to make to the MAV before he arrives. I just think no one was willing to take the Space Pirate moment away from him... although Teddy would have to have been tempted to get some revenge for the pair of boobs moment.
And while he's driving there, he did mention the space pirate thing to NASA, which led to Victor having his 'strange minds think alike' moment. And then they tell Mark about the modifications he'll have to make to the MAV before he arrives. I just think no one was willing to take the Space Pirate moment away from him... although Teddy would have to have been tempted to get some revenge for the pair of boobs moment.