One point I want to make about your thought provoking post is that unless they were prisoners, I think it likely that most of the men who died of disease, (or even mortally wounded died later) especially at military posts and hospitals, would be most likely to have been buried with better account of their burial than a KIA, at least much better than the battlefield burials. It would be my guess that the majority of Unknowns would be either KIAs or POWs. So any detailed lists by regiment of both KIA and POWs might go a long way to at least putting names to many of the Unknowns.
Men who died of disease, while certainly equally deserving to be remembered, might be more apt to be buried, even possibly as Unknown, at places like Mound City than at Donelson, and can perhaps be listed there as "possible Unknowns".
I was just thinking out loud I guess with my suggestion, but it seems like when the NPS lists burials at a battlefield like Donelson and then say something like "plus 500 Unknowns" might at least begin a list of those names of men known to have been killed and buried in the battle as "probably among those 500" are XXX and XXX.