"Earlier posts in this thread suggest that Confederate reports from the company level and up don't accurately represent commands on the field."

Brigade commanders certainly knew how many men they had present for duty on any given day, since it's known that the company morning reports from the component regiments went at least that far up the chain of command. I can't speak with any authority on division or higher. I presume, but don't know for certain, that divisions received summaries of morning reports from the brigades. I vaguely recall reading something about morning reports (or a summary thereof) being received at corps headquarters, but I can't remember if this was a daily occurence or not.

However, I can see where the commander of another army or department might not have accurate information as to the actual strength of a division in another army or department. Timely communications between armies and departments -- especially between the Trans-Mississippi and the other armies -- was a persistent problem.