The accounting systems used in DoD today (BQ & CRIS being 2 of the biguns) were not designed to do what you're asking it to do. And they were definitely not designed to comply with gaap. In that sense, you're right and the expenditures will never balance to a purchase. Esp when you consider all that goes into a program office and testing, facilities and what not. When you try to amortize all of those other costs to eventually buy a hammer, that is literally how you end up with a 100 dollar hammer. (and it is probably nuke certified lol)
I am NOT saying there isn't problems with how DoD spends money ... I love Newt's line at the F-22 rollout outside of ATL ..."let's turn the Pentagon into a triangle".
There is where the problem lies IMO. When Executive staffs are manned at 100% and Command staffs are manned at 90% and actual execution staffs manned at 60%, AND the only way the "Executive staff" member gets ahead is by creating a new policy ... you end up with a bunch of dumbass policies and no one to ever execute it fully (sometimes a good thing!) nor adequate time to train or understand. They can tell you where $$ went in terms of contractor, test event, sub-contractors, manpower, TDY, but not in terms of one asset.