Why not just stick it in the flu vaccine then?

I'm thinking it's because the vaccine was designed to interface with the virus itself. Or, the vaccine was created before the virus. This video points out that the virus produces tentacle-like structures. The vaccine also produces these structures, which suggests that they interface in some way. It's all still being researched. First thing I thought of, is the analogy of a public and private key.

I tend to disagree with your other points, because this tech has been in development since at least the 1950's, possibly even earlier. Remember, compartmentalization is very effective for these black projects. The scientists do not know the bigger picture of what they're working on.