Is 18F sufficiently independent, or this project sufficiently below the radar that it just isn't an issue?
People think "The Federal Government" is a monolith, and they could not be more mistaken. It is a collection of individual entities, operating largely independently and often at odds with one another. 18F is a different entity with a different set of goals from the law enforcement (FBI/DEA/etc.) and intelligence (NSA/CIA/GeoInt) agencies.
In any case, it's also different parts of the tech stack - encrypting everything over the wire with HTTPS is fine so long as the underlying encryption is weak and/or the NSA have a set of keys. The FBI can always just issue a national security letter to the party with whom you are communicating.
That's definitely an accurate description of the US federal government.
Nothing below the radar about it:
https://www.whitehouse.gov/blog/2015/06/08/https-everywhere-...