Do you have a source for that? The article you linked does not promote this thinly-veiled conspiracy theory.
Here is a link to the satelite agency having enough funds in a secret slush fund that they avoided the budget process and simply bought land and built a top-dollar building. No accountability in early 1990s! https://www.washingtonpost.com/archive/politics/1994/08/10/b...
A few years ago the Admiral who was Chairman of the Joint Chiefs shocked me by publicly throwing out the number (if I remember correctly) of $7 trillion that the DoD couldn’t account for. That would buy a lot of lunches for hungry children in our country. Anyway I was shocked by his admission, although I think his estimate is too low.
What our country needs is more patriotic people like that Admiral who at least occasionally inform the public.
Budget is what they ask Congress to put in spending bill which is signed into law. Then funds are appropriated. Then funds are spent. Pentagon spending audit is overdue by a couple decades. https://text.npr.org/997961646
Donald Rumsfeld gave a speech and pledged to get to the bottom of the missing $2.3T. He even created office space just for that effort and put everything there so the bookkeepers could get the job done. Guess where the Pentagon was hit the very next day? https://www.cbsnews.com/news/the-war-on-waste/#app