Your counter example is poor. Flynn holds a degree in a related (but not closely related) field. He holds a PhD from a real university. He has published in the leading journals for his area of research.
The only possible way he triggers any of these red flags is a degree in sociology rather than psychology. These are red flags calling for more scrutiny, not strict conditions. And indeed, it seems like Flynn does deserve more scrutiny. He's clearly a legitimate scientist doing important work, but this is despite the red flag of being someone from a different field offering up theories that go against previously established science. He shares several of the quickly observable features of a crank.
How do we know he isn't a crank? Because he's published in the leading journals and other scientists who meet the "not a crank" test have said that his work is worthwhile.
In short, this is not a false alarm by the "red flags". This is a correct alarm.
A lot of physics quackery comes from engineers.* Their knowledge of advance physics is generally nowhere near that of a physics PhD, but their title lends them credibility to many people.
I don't know about physics, but a few years ago here in Argentina there was a epidemy of "engineers that solved the Goldbach conjecture". A few (¿maybe 5?) of my math Ph.d. students friends had each one his/her own engineer with a different unrelated proof.
The histories where all different, but generally it was a long (100 pages) proof that was involved and not very clear. So the math Ph.d. student and the engineer meet weekly for one year to try to understand the proof. It was very painful because they have to understand which part was only unclear or has only small gaps, and which parts had errors that were impossible to fix. And then they had to explain that to the engineer, that were happy to had solved the conjecture.
All of this is in a scientific field that there isn't too much money, press coverage or social prestige involved (not like a "cure for cancer"). So I think that in more applicable fields the problem is worse.
The only possible way he triggers any of these red flags is a degree in sociology rather than psychology. These are red flags calling for more scrutiny, not strict conditions. And indeed, it seems like Flynn does deserve more scrutiny. He's clearly a legitimate scientist doing important work, but this is despite the red flag of being someone from a different field offering up theories that go against previously established science. He shares several of the quickly observable features of a crank.
How do we know he isn't a crank? Because he's published in the leading journals and other scientists who meet the "not a crank" test have said that his work is worthwhile.
In short, this is not a false alarm by the "red flags". This is a correct alarm.