Changed rusty liftgate with the same year 2011 escape xlt. Alignment at roof line of gate is 1/4” high on the left side and 1/2” high on right side. Also right side is 1/2 “ away from outer weather seal.
Those are massive misalignments. Do you still have the hatch you removed? I would carefully compare measurements taken from both hatches.
NOTE: I just bot a 2010 and the owner included a nice southern rust free hatch. It looked like it was the proper hatch, but it turned out to be a Gen 1 which is different when you look carefully. I don't know what would happen if one tried to install a G1 hatch - might this be your problem?