"It" here refers to "F35 budget". The punctuation is not ideal; I think it would be clearer something like this:

> With the F35 budget well over a trillion dollars (this is 2-3 orders of magnitude larger than needed to fund maximum number of projects Skunk works can sustain, at max manpower), it is a bureaucratic waste with minimum productive output.

The word "Skunk" does not start a new sentence. It is in the middle of this phrase: "this is 2-3 orders of magnitude larger than needed to fund maximum number of projects Skunk works can sustain". I'll agree that the punctuation isn't ideal; that phrase should have been preceded by a comma.

The poster you are responding to is correct. Sorry, I could have been clearer in wording and "it"s.

Skunkworks is great, but works while it is small and nimble. Fund it fully. But this could cost billions, tens of billions at most. Not trillions that have been spent on F-35.