Is that 45 mm deep before the step-down to the clearance hole for a long bolt or stud?
I agree that some shim (preferably hard-rolled brass, about 0.005" thick) would probably prevent the nut from being bruised.
You are doing all the right things and preparing properly, it's just that in your picture the thing looked brand new and it would be nice if it stayed that way. If it were just a run-of-the-mill one that has already been unscrewed with a Stillson half a dozen times, you'd be over-prepared, if anything.
