I don't believe for a second that 911 was a grand conspiracy and find most of these theories utterly preposterous. But I can certainly envisage a viable, if entirely imaginary scenario were it could have been run like a military or intelligence operation with perhaps 10s or hundreds of people directly involved.
No, it couldn't.
Both those bodies are inherently good at keeping secrets
Not that good.
You used the Bletchley Park example. You are aware that one of the security officers at at Bletchley Park was Kim Philby, the noted Soviet spy? Stalin had better access to BP material than Roosevelt, because Roosevelt had to go through British channels; Philby could simply help himself to anything he liked. The "secrecy" of the Bletchley Park project was breached almost from the start, because there are/were people whose loyalties were to other groups than the project.
Fortunately for the conduct of the war, everyone involved seems to have been loyal to the idea of
winning the war, so they didn't tell any of the Germans or Japanese about it. They also generally knew exactly what they were doing and knew why it was important not to tell the Axis about their work. Even after the war, the honest patriots could be expected to keep their mouths shut because they knew how important SIGINT still was during the Cold War.
An "honest patriot" asked to rig explosives in the WTC would either have to be told the big picture (in which case he would be highly likely to spill the beans) or would have to be left in the dark,... in which case, he would know as soon as the event happened what he had been involved in and he'd be highly likely to spill the beans.
What happened.
and when you factor in self incrimination it's not massively implausible that it could be kept secret.
Hardly. A whistleblower could easily arrange immunity from prosecution.... if necessary, just flee to another country and seek asylum.
If it was left entirely to the Nazis I doubt we would have found out about the holocaust, as the participants were fully intent on keeping it totally secret.
Actually, "we" (Allied intelligence) knew about the Holocaust in 1943. The Jews knew about the Holocaust more or less as soon as it started happening, but there wasn't much to be done about it at the time.
Another really bad example -- or really good example about how you can't keep a conspiracy of that size secret without active buy-in from everyone involved.