While the idea of some gov/agency involvement in BitCoin is not entirely far-fetched, the code/algorithm itself is fairly simple and doing what it claims. The likelihood of backdoors or non-understood effects is small.
A greater possibility is that the entire bitcoin concept/operation has been created and supported for some generally unknown further purpose.
And thinking that some shady organization will have a plan like "Hey, lets build a great technology with the power to substitute the entire economic system and unleash it into the wild and lose complete control over it and maybe it will gain enough popularity and maybe some day, some how we will be capable of harnessing its power to do something", that's tin foil hat mentality big time.
There are way more popular and widely used open source software and I don't see the nutjobs making outrageous claims about them, like linux, apache, android, open office, and so on, well we see then making claims, but not as much as with bitcoin technology.
The difference between the open-source projects you mention and Bitcoin, is that they have known developers and founders, while "Satoshi Nakamoto" is not a known individual. To invent an algorithmic design of this caliber out of the blue, document it in a published paper, develop it in software, engineer and test into a working system scalable across millions of machines, release and sustain the seed operation over a period of years, all the while maintaining total anonymity, and ultimately perfectly disappearing from the scene without a trace... speaks to a very wide skillset, dedication, and resources -- arguably beyond any 1 person's capacity.
By the way, I wonder if you realize, your quoted example of a crazy plan: "Hey let's build... unleash to the wild... harnessing it's power" is a not too inaccurate description of the internet itself (originally a Darpa project).
Bitcoin mining is not "a cover". It does what it says it does, which is pretty clear, and very useful. No reason not to move forward with this great technology. (although energy inefficient). For those asking "who has verified it?", many people. There is an extended development team and many other academics, researchers, engineers and developers who understand it to varying degrees (including many on this forum). It's not some arcane black box.
However, there are certainly interesting questions about the origin, why, who, is there an overall "schedule/program" of some kind, is it a testbed for something future, what does Mark II look like, etc. And as for many cryptographic technologies, there could be advanced exploits/holes that are beyond current state-of-art. (of course, if they break Bitcoin, they probably break a considerable number of other things too).