How could it be a violation of the Logan Act? That would infer that the POTUS elect and his transition team would not be authorized to negotiate with foreign governments and makes no sense. This is just Flynn trying to get some reduced charges\sentence. If you have some case law that you can site that disproves this please provide it, because I can guarantee you this in not the first time a POTUS elect has contact foreign governments
This is where the "seedy ties with Russia" come in. There's a lot still up in the air, but as far back as the beginning of the year, we knew that trump administration officials had behaved illegally. In the simplest terms, Flynn is being charged with lying.But one train of logic goes like this:
1)The gov't believes there is evidence that this foreign power illegally hacked into one candidate's email, which ended up being a major factor in the presidential election.
2) You have an administration willing to negotiate with a foreign power during a prohibited period, which suggests pre-existing contact.
The administration lies about prohibited negotiations, which further supports the theory of pre-existing contact.
3) The question becomes how much pre-existing contact was there and did that contact play a part in the hacking? Was there knowledge or coordination beforehand? If so this is very serious- administration contacts committed a crime to sway the election and then began favorable negotiations during a prohibited time frame.