I think we’ve been going about this wrong. Comey and the FBI had set up an illegal wiretap of Flynn in order to get dirt on him so they could make sure he wouldn’t be Trump’s Intelligence Chief. Flynn knew where all the skeletons were buried with regard to Obama’s illegal Iran dealings and the gun running in Benghazi. If Flynn were ever to have control of the intelligence apparatus, they’d all go down.
They “by the book” reference is to make sure it “appears” Flynn’s name was inadvertently discovered during routine monitoring of Kislyak. That way, they can say they unmasked Flynn as a direct result of the legal monitoring as opposed to the illegal wiretaps of Flynn that they already had in place. I think that’s why the “by the book” reference is in quotes. They had to make sure it looked like a legal intercept rather than an illegal one.
The only reason for a “by the book” reference is CYA because it wasn’t by the book.
It’s outrageous we still do not have the basic facts of the Flynn entrapment a year after Barr became AG and 3 1/2 years after the event.