o wow first pic i didnt even realize you were showing the back of the x pipe lol...
those look like maybe someone welded the intermediate pipes onto the muffler slightly crooked if i had to guess. when i had my old flowmasters i had to twist them a certain amount otherwise id have a sagging issue, then that would also twist my tails so you may want to look into getting a full cat back system. im fairly certain a flowmaster cat back will line up better than that, unless that is a full flowmaster...
it just looks to me like a crooked weld on those intermediate's, they are angled a certain way. yours look up and down to much when they should be side to side, if that makes any sense. just turn the pipe (in your head) 90 degrees and you should see what i mean