Mine look like that. You can mess with it and get it "straighter", but it's not worth the time. Mine don't leak and have never had any problems. Showed it to the dealer once...we walked the lot and saw about every other Jeep had the same (non)-issue.
To me, it's simply a QC issue on Jeeps part, but doesn't really affect anything.
Lift it high enough, you'll never see it.
2013 Commando Green JK Rubicon
Remember - sometimes, the advice you get on the Internet is worth exactly what you paid for it!
Funny, this just happened to me last night. Have had freedom tops out several times and reinstalled w/ no problem. Last night, it was like the roll bar had been bent or moved. Would not line up. Got pissed and just beat it into place! Still not right and I had wind noise that I have not had in past. Going to take off and reinstall once I get garage heated up! Getting into 20's tonight.
Mine are the same, actually there probably even further off than yours are. I never really worried about it cause its never leaked (in fact in two years my jeep has not leaked anywhere, knock on wood, and she sets outside to boot).
I tried to align them closer but with the pins you can only move them so far. Like knuckles said its prolly just a QC issue and I dont see it as a problem.
2012 Crush JK Rubicon. Teraflex 2.5" coil w/fox shocks & 1" rear TF spacers. TF monster front and rear track bar. 315 75r16 duratracs on level 8 zx wheels. LOD armor lite mid w/engo 10000s. Lots of other goodies.