In my simpler frame of reference, I believe the major difference between civvy and camo is the specification.
Military aircraft meet the military's specifications. If the spec is screwed up, so is the aircraft. Often improvements are not included as they are "not in the spec". Safety is never usually an issue, and as Nick says, ballistics are often a factor - but of course they are usually in the spec.
The FAA cares about safety - no laffing please - but essentially they can say " as long as it's safe, we don't care if it has a range of 8 miles and carries 2 people" - as long as it was intended to have a range of 8 miles and carry 2 people! It must meet it's intended function.
The Market will determine the other features that are traditionally in a spec - range, cost, payload etc.
So a commercial manufacturer will strive to get the best performance (or DOC or whatever) so that he can sell it - the FAA ensures it is safe.
Now, IF your design anticipated military requirements while designing a commercial helicopter, but don't burden the commercial viability - you have a winner.
just watch the S-92 - trust me.