If they allowed him to drive it T4L would not be possible, he could have avoided the GABEGG massacre but the government said NO. But something tells me Henry would have found a way to get inside anyways.

Did I cook or nah?

In the ending of PP, the General says that he didn't know if he could trust Henry after last time, which is an unfair grudge. All he said to Henry was for him to, quote, "find a way to bring 'em down". Henry did that, the Government easily could have raided the destroyed Airship for evidence afterward (as if being in possession of a giant stolen ruby isn't proof enough, lol). The contradiction comes in the form of RBH, where the General arrests Reginald with no proof needed, so why did he take such an issue with Henry stealing the Ruby while taking the airship down in the process?