High end clays shotguns come with pads. A Belgium Browning can be ordered with a pad, so diminishing the value is a debatable issue. They also can be ordered with a desired LOP. Again the same situation.
If a pad is desired, then have one of quality installed, at a LOP that fits by a Smith who knows how to do it right....many don't... and go on and enjoy the shotgun. High end Krieghoff, Perazzi, Kolar and Brownings come with pads. And the owners often have them cut to their desired LOP without diminishing the value, other than the shotgun is a used example.
However if originality is a concern and the stock was cut, keep the piece and plate that was on it. A good Smith can put it back on, and since the grain matches, it would be difficult to tell when refinished.
Addition: Keep in mind they even gave the MonaLisa a refresh.
