Don't laugh but at this point my working theory about @GenFlynn and the Logan Act is that the people in the Obama administration got the idea from the freaking West Wing cable TV show

An episode at the end of the series ("Transition") shows the outgoing lame duck admin in a foreign policy dispute with China and Russia. They carry out electronic surveillance of all calls with Russia and wiretap the incoming team and confront them about...

...the Logan Act!

That theory - while it sounds nuts - is actually more plausible than the other two:

a) The Obama FBI or Justice Dept. thinking they could prosecute the Logan Act against anyone, let alone an incoming National Security Advisor

b) Joe Biden even knowing what the Logan Act is