You have to fit the trim sometimes to car like you mentioned. Removing the trim can warp it, and it depends on what the buffer guy did as well. Never goes back on perfect most of the time. I have installed my trim in which I have a 67 cuda and converted it to 68 stainless trim... long story.... and going to have to take mine back off and make adjustments. So I know exactly what you're talking about. Might have to take it off and on many times.
There are a few tricks that make it fit good again. I have seen where the back of the trim was cut/notched so it would bend easier and therefore lay down... look good. Block of wood and rubber hammer works too.... but you might think I'm crazy. Some of the older cars have massive trim that doesn't bend easily.