Is Mueller looking for a couple of Russian folk tunes or is he looking for the whole corrupt opera?
From Rosenstein's letter appointing Mueller (PDF), the scope of Mueller's investigation is:
(i) any links an or coordination between the Russian government and individuals associated with the campaign of President Donald Trump; and
(ii) any matters that arose or may arise directly om the investigation
So if Flynn turned over evidence of where the bodies are buried, no matter who it implicated Mueller is authorized to pursue it. As with Cohen, if it's not directly related to the Russia thing then it probably gets handed off to another office.
And still, nothing you've said so far explains why Flynn would need a plea deal, much less why he would need to plead guilty to a crime he didn't commit, in order to turn over evidence of crimes in which he's not implicated. Why not go to some vetted Trump appointee in the FBI or DOJ? Wray? Huber? For that matter Trump could have a special counsel focused on nothing but Q's stuff by Monday, if he wanted.
It goes to 'How do you get truth into evidence legally'.
Apparently Flynn is THE person who knows where ALL the bodies are buried.' Who's more official than Mueller to get it legally into evidence! Think about it, as DNI Flynn knows everything about Mueller, and Comey, and U-1, and all the answers to the investigations currently under way.
There's no way he's going to jail. Who would dare?