Firstly, that's the way large US govt contracts play out. Command obviously hasn't made the HR investment necessary to put a stop to all the interference or have the work sent to them as subcontractors. Like it or not you've got to have some ex-military brass and political types on payroll, at least as consultants. That's the way it works.
That being said, it's shit that it works that way. Having former insiders working with you used to be all about getting a little heads up on upcoming bid opportunities and how the agency watnted proposals positioned to meet their mandates. That's how its worked since WWII, and it wasn't especially crooked or shady. You weren't learning anything you wouldn't if you did the regular DC dinner, drinks, donation rounds, you just did it by proxy, through your consultant(s). It's all different now though, especially after 9/11, it's all shady as hell.
I put most of the blame on the big push to 'shrink the size of the Federal government'. They just outsourced all the jobs, the government isn't smaller snd it's a lot more expensive. Anyway, individual agencies and military branches outsource almost every aspect of a project to one or two primary contractors and let them handle the distribution of subcontract jobs. It'll be somebody at DoD or GSA who signs off but it'll be signing off on whatever the primary contractor hands them.
There is no core competency left in the government. Project drafts read like a 5 year olds wet dream: 'We need a plane that goes Mach 9,000, a range of at least eleventybillion miles, can destroy everything and is really quiet. Oh yeah, it has to fly and not kill the pilot every time. Here's a blank check, go build the new plane."
The organization that will eventually be a primary cooks up something somewhat resembling the draft specs and already has its supply chain figured out before they even submit the proposal. If you aren't in on the initial proposal you aren't getting in. One or two primary contractors control quite nearly 100% of a project, the government just signs the checks, they don't even know what they've really commissioned. Just that it'll be 'superior' and that it'll provide (x) private sector jobs.
It's all crooked as hell and chances are that Lockheed is correct, the judgement won't stand upon review. If Command manages to keep its doors open they'll get tossed a few bones in the future, but it'll be for crap like 'sanitization of flight suits following high-G maneuvers preceded by chicken vindaloo meals'. They'll also get lots of people knocking on their doors to assist them in streamlining future contracts.