Project Chapel Bell is still classified, though widely rumored to relate to over-the-horizon radar. Not even the astronauts were told what it was, only that it pertained to the launch vehicle only and not their mission. A lot of the bits of Apollo were classified for obvious reasons: they dealt with U.S. missile capability. Some, like the low-light television pickup tubes, were just sort of handed to Apollo under the table from Defense without talking a lot about it. The debriefings were classified for a standard 25 years because they dealt with the crew's private health information. They were automatically declassified according to a standard stand-down schedule.
That illustrates really how it works. The actual astronauts who flew in the rocket were still not code-word cleared to know some aspects of the missions. Sure, they knew a lot about how the rockets worked, and therefore had to have the appropriate general clearance levels. But operational security works on a need-to-know basis. Even an engineer who needed access to the mission debriefing while it was still classified was probably likely to be given a version from which private crew information had been redacted. He may be Top Secret cleared to read the technical material, and code-word cleared to get the precise information he needs, but that doesn't given him access to information he does not need to know. A schema to map Dept. of Energy clearances to those in other agencies is kind of a red herring. It doesn't capture what really goes on.
