At Signature at Logan, I had to go through formal non-FBO security (including a metal detector) in our Part 91 light piston single. I’m virtually certain it was TSA (but could have been contracted).

I’ve had metal detector and uniformed security treatment at some other class Bs and even at Wheeling, WV (which was entirely out of place compared to the scale of that airport).

In any case, even if it’s just the crew that has to validate your ID, that still prevents you from traveling as anonymously as you like, doesn’t it?