It now feels like Johnny is working against Duffy. Not because he loves Boyd, but because he wants to break off and start his own illegal entrepreneurial enterprises. Hence, why he's trying to get money from Colt and why he wanted to show that prostitute that he's able to take care of business.
He's obviously aware that Boyd wants to get into a legitimate life and is probably going to use the respect/power he's been saving up as leverage to get Boyd to hand over all the keys he ain't using anymore. Boyd will probably agree, but then the last thing Boyd needs to do is maybe go after Wynn Duffy since Boyd is now on the Dixie Mafia shitlist for not delivering Drew. If they want to end the season with a tragedy, it would make sense for Johnny to get killed in all this.
As for Drew Johnson, he seems like he's become a good person now and is probably not going to use anybody as a pawn, and I'm betting he has a good amount of cash and fake ID papers stashed away. I wouldn't even be surprised if he stole the constable's "bug-out bag" while Raylan was still piecing it all together. I do wonder if he's going to make a visit to his ex-wife.