You can trim if you like, but the actual problem here is in the door liner itself. I was just kidding about the "magical warping". It is a real possibility, but not from the service you performed. It is normal for a certain amount of frost to accumulate in the recesses under the dispenser chute, especially around the drive mechanism for the augur. Once this ice begins forming there, it actually distorts the door chute area where the bin sits. The bin is still OK.
The recourse is a new door and seal it well around the area where the tubing comes into the door to prevent air infiltration. I had actually gotten so good with a hair dryer that I could heat the area up and warp it back into shape, but this is not for amateurs unless you already plan on a new door assembly.
The part for the complete door on your model is L2216604W and unfortunately the liner is not available separately.