expansion from heat is the only thing i can logically think of causing the issue. car is an 04 vw gti. I actually cut my patch panels from a spare vw oem hood that i had at the shop so i know its all the same material. and for expansion i figured the patch that has the coat of duraglass over it wouldn't be an issue but it didn't make a difference.
Not my car (no pics of when i did mine), but i did the same job. shaved the door handle pockets. also shaved the handle completely on the hatch but that was just a 3"x5" rectangle opening