Rework rifles vs rework pistols are different animals, but of the same breed I suppose. A few points:
Commercial proofing was only necessary if some part of the locking assembly was replaced, this according to German proof law. On a rifle the bolt, barrel and receiver were proof tested. On a Luger? A new barrel would require proofing, or a new unproofed bolt head? Maybe receiver. BUT - some parts were supplied already proofed, for the K98k the bolts were pre-proofed, so a 98k that got a new bolt would not need reproofing. Receivers and Barrels were not pre-proofed on the k98k, so replacement of either would require proofing. I know replacement P.38 barrels were pre-proofed by the manufacturer, along with slides and frames. On the Luger, barrels were NOT pre-proofed, I'm not sure about bolt heads and frames.
So, on a Luger for instance, a new barrel would require reproofing, and a new Crown N would be applied to the barrel i assume (I have a reworked Luger with a new barrel and the barrel has a normal Nazi test proof, it's an Army rework though and Army depots had permission to pressure test proof items). The SS DID NOT HAVE THAT PERMISSION, so any re-proofing would necessarily be commercial style proofing. Even though the SS were criminals, they did (mostly) follow proofing laws, there are examples which defy this authority but generally they followed the proof laws.
A Luger reworked by an SS depot that had a barrel replaced would need Crown N/ Eagle N inspection to be legal.
About what got marked in depots - as I said, I have not studied the deaths head Lugers to any degree, I know about them but I assumed the Luger guys considered them SS reworks just based on the similarity to Gew.98 reworks, I guess I was wrong. Anyway, It's very possible that a batch of them were reworked/inspected, and any that went through the depot could have been marked even without any substantial rework. If it helps, I have seen 98k rifles with no discernible work done having Army depot marks, or minuscule work done. If a rifle was having accuracy issues and was not repairable in the Feld-Werkstatt, it was sent to a higher depot. Perhaps a stock was warped, or sights were simply out of alignment, or maybe a barrel not perfectly straight. These could potentially be repaired without any parts replacement, but still receive a depot mark. Was it the same for SS depot work? I admit that I don't know.
About the "Lazy S" skull on Gew.98 rifles. I just started a thread today about those. Nobody has documentation to prove anything, but the two main SS depots prior to 1940 were at Dachau (Munich) and Sachsenhausen (Oranienburg). The 2 most common skull markings seen are "Lazy S" and "Gull wing". My theory is the "Lazy S" is Sachsenhausen, which makes sense as it was the main SS depot, right outside of Berlin. The other "Gull Wing" skull marking looks like a flattened "M" - Munich perhaps? It makes total sense that the 2 main depots closely match those markings, but I fully admit my thoughts on that are a work in progress.
So the question about why there are no later depot marked Lugers - the "Lazy S" marking was replaced by about 1937/38 from memory, before any new Mauser made Lugers would have been issued to the Waffen-SS, and once the SS was under Army command the Army depot system was available to them for repair work, and they used them. The SS depots were still active, but generally were reworking guns used by units other than the Waffen-SS. Actual Army marked guns with SS depot repairs are pretty scarce, but as you state do exist. Also, the SS got the worst of the stuff available, probably very few of the newer Weimar Lugers made it to them.
There were depots in the Army system that specialized, and one (Ingolstadt) was for Pistols, the majority of reworked pistols I see have that depot marking. Perhaps the SS did the same thing? It would make sense. The whole idea of reworks is a complicated issue, it takes a lot of careful consideration of each reworked item you find to "verify". You almost have to just collect reworks to know you are getting stuff that is good, so you can have multiple examples to compare them with. I'd hate to be that guy collecting deaths head Lugers.