Meyer,
Could you take a thin metal ruler and (carefully) take a measurement at the crease of pinch weld to the back window and check the length of the portion of the clip that is sticking out under the glass seal. Compare that length with one of your old original clips and see if they match. Because there are two different lengths to those style clips and I just want to rule that out (excuse the pun). It's either the length of that part of the clip is the shorter one or the thickness of the rear glass seal that might be not allowing the trim to reach the clips. I don't think the slight deformation of your trim is causing it.
Could you take a thin metal ruler and (carefully) take a measurement at the crease of pinch weld to the back window and check the length of the portion of the clip that is sticking out under the glass seal. Compare that length with one of your old original clips and see if they match. Because there are two different lengths to those style clips and I just want to rule that out (excuse the pun). It's either the length of that part of the clip is the shorter one or the thickness of the rear glass seal that might be not allowing the trim to reach the clips. I don't think the slight deformation of your trim is causing it.