Mueller stated he's a subject, not a target, currently. The charges are well within the purview, since Manafort had previously worked on the election of a pro-Russian candidate in a Ukraine election. Some of the evidence against him was obtained from other subjects and witnesses in the investigation, like his former partner. Rosenstein gave him broad authority and has to authorize new avenues.
"Yeah, I'm guilty of bank fraud and money laundering, but it happened before I was in the campaign." That's a weak defense and pretty much a legal Hail Mary. Current guidelines for special counsel appointments are against him. Manafort probably doesn't have anything to trade away. He's screwed himself by being crooked as well as a lousy advisor/campaign manager. He'll have nothing to show for it, but a new jumpsuit.