I bought a lead sled several years ago, and right after I bought it, I too heard rumors of stocks cracking at the wrist, being scratched heavily on the sides of the stock from the sled also.
So I took the protective cover off the back of it where you put the rifle butt, and glued in some protection to ease the thrust of the wood stock against the steel. I obtained some heavy duty styrofoam from a local craft store, and glued in on the inside walls, 1/2 inch thick on the bottom and back, and 1/4 inch on the sidewalls. The protectiove cover then fits nice and snug over the whole setup. As an additional plus, this holds the gun in place much more firmly, with no side to side slop.
We use the lead sled primarily for sighting in 12 gauge slug guns, and they recoil pretty darn hard, especially those 3 inch slugs. We've never had a problem, or any damage of any kind to any of the guns, and haven't seen any change in impact shooting the gun otherwise after sighting in on the lead sled.
We use the lead sled as is, with no weight of any kind on the tray, it's simply not needed, and I believe, if you do make the sled to heavy, it could be detrimental to the stock. The idea is to reduce recoil, not make it a solid machine rest, and the sled itself is heavy enough by itself to do just that. Used on a smooth bench, the sled will move backwards and recoil mildly into your shoulder at the shot, which is just what you want, so in effect, you're adding weight to the gun(via the sled) and not making it a solid machine rest.
Believe me, I have some slug guns with custom wood I have built, and in some cases, the wood is worth as much, if not more than the rest of the gun, and if I thought the lead sled was going to damage them in any way, there's no way I'd use it, but we've used it sighting in a goodly number of 12 gauge slug guns(all with wood stocks), in some cases over 100 rounds per gun in the sled, and never an issue. It is vastly superior to sandbags, in my opinion for doing fine tuned sighting in.
Number 1 son sighted in his Ithaca 37 smooth bore slug gun on the lead sled, then, last Monday afternoon, proceeded to take a large doe at 129 lasered yards shooting sitting down, offhand, military style with his left arm tightly wrapped in the sling, no change in impact at all, one shot, bang flop, a very dead doe.