I don't have much to base this on other than a gut feeling based on having been around these, but I strongly suspect that the capture X was unrelated to the larger refurb process.
The X was a capture mark independent of the refurb process. There are plenty of examples of VoPo K43s, K98ks, pistols, etc that have the X mark but didn't go through the rest of the refurb process that we're familiar with from the RCs and the assorted cold war refurbed Soviet arms (mosins, SVTs, etc).
Given the security concerns of the time, my best guess is that the capture X was similar to the "1920" mark you see on Imperial arms - a property mark to indicate that the gun had been through some level of government control. Keep in mind ,everyone was terrified about the potential of a Nazi resistance movement in the late war / immediate post-war era. In a hypothetical where you kill a few people trying to blow up a rail yard or something, it helps to know if they got their guns from the general cloud of arms floating around following a major conflict or if your warehouses of captured goods are leaking. Again, that was the basic thought behind the 1920 marks.
Given that, it the lack of capture marks on some soviet arms makes a lot more sense. The soviets captured arms both during the war and in the mass surrenders at the end. My opinion is that the arms lacking the "X" are the ones that were captured during the war and stuck in some warehouse in Belarus or wherever. while the ones with the stamp were the ones brought in closer to the end of hostilities.
This is naked speculation on my part, but I do think it isn't completely baseless. At the very least I will stand on the refurb process and the capture X stamp being totally unrelated.
