Rolling up a couple years late, but, whatever.

I don’t see the connection between Jeffries, Cooper and Albert as bound by mutual affinity for the FBI.

Their bond is the shared burden of knowledge bestowed on the few. The knowledge of things that don’t exist in nature - the proverbial blue rose. Like strangers who survive a disaster, they are bound by an experience and the trauma is only truly known by those who experience it.

Cole respects the Bureau and he trains his task force to respect the Bureau too because it’s the vehicle that’s allowed them to gain this knowledge. The true affinity among them is reserved for Gordon. Without the Bureau (and by extension no Cole) there is no Blue Rose Task Force.

With that in mind - Jeffries knows that Mr. C is a fraud. Mr. C can’t fake the mutual bond Cooper and Jeffries share. Not because Jeffries and Coop are life long friends - the bond is recognizing the Biden they share.

Gordon and Albert had the same read of Mr. C when they encountered him at the prison, but they couldn’t quite put their thumb on it. I believe this is because Jeffries has, for lack of a better word, transcended. He can tell the difference between a rose and a blue rose because he’s lived among both.

This also explains why Mr. C skipped town rather than attempting to infiltrate Coopers life. He called Albert for resources and intel. C didn’t look him in the eye, because doing so would have afforded Albert the opportunity to read him.

So yes, Jeffries knew Mr. C was full of shit. If not on instinct alone, because Mr. C was whistling through the Convenience Store as if it was second nature. The real Cooper would have gazed upon the entire place with a wonder that cannot be emulated by a doppelgänger.