I went through a fair amount of xeons (just bought different steppings didnt fry em or anything
) and all of em tended to leave marks on the stock coolers. The aluminum bases of the stock heatsinks tended to get marks from ther corners of the IHS just like your DX got. Some were more concave than others. They never marked up my mcw5002s though. Used the same spring clips so it was the same amount of force. Guess the aluminum was just softer? Guess your TDX springs are pretty stiff.
If you are going to remove the IHS and lap it why not just remove it and make a shim so you can mount the wb directly to the die?