I have built class 8 trucks for 29 years, there is no such thing as a perfect vehicle.
They put that on the passenger side on purpose because inspectors are trained to view things from the drivers perspective. When I picked my Jeep up from the dealer the passenger side rear wheel molding fit poorly. One smack from the palm of my hand and it popped into place.
I don't like the way my sunroof fits, not flush on the front corners. However, it doesn't leak and I live in Oregon. Give it a water test with a hose, if it is leak free I wouldn't worry. The pressure of the roof being closed should provide an adequate seal.
They ram those things down the line like you wouldn't believe.
2011 LAREDO X Hemi, Offroad Adventure II, QuadraDrive II, Quadra-Lift, Trailer Tow IV, Factory 18" wheel delete, TOYO ATII 245/70/17, Charcoal Pearlcoat, Black Leather, 430N, Single Pane Sunroof http://www.jeepgarage.org/showpost.p...7&postcount=16
2011 TOYOTA TACOMA TRD OFFROAD (wife's) & 1989 TOYOTA DELUXE PICK-UP (had since new)
previous JEEP 2004 LIBERTY Rocky Mountain (R.I.P)