^^^ Not sure I get the point you're making, it's no secret he took the Devil charge for Boyd whom he apparently regards as family and judging from his first encounter with Raylan at the bar when he looked disappointed and made the comment about hearing a cop with a hat had been killed, the confession of having shot a cop with a hat pointing a gun at Boyd seems in no way suspicious to me
When Boyd was in jail for blowing up the Sheriff's car Johnny's comment to Ava about them sticking together seemed less than innocent and now we learn that he's holding a grudge about taking a shotgun blast to the gut, really looking forward to watching that play out
After having proven himself honorable with respect to the Bennett money Limehouse also proved himself a man to hold a grudge, his 2nd in command Errol started this whole play for a bigger piece of the pie which led to confrontations with the Crowder crew along with associations with Quarrels and unwelcome scrutiny from the Marshall's service but the second the threats subsided he got rid of him...but there's still the issue of the moves made against Boyd which are far from resolved or forgotten
All said and done great season though if they had found a reason to kill Duffie that would not have bothered me