Yeah, except it wasn't. At least everyone that was actually there says it was further south rather than in the hospital with the surgeons hacking off limbs. There is some discussion whether it was the Ecker knoll or another one to the north, but the evidence is clear it wasn't the Pry House.
"49. Strother, "Personal Recollections," 281. There are two possible locations for this command post. The first is a knoll located just across the Boonsboro Pike to the south and east of the modern entrance to the Pry House, next to the modern First Baptist Church of Sharpsburg. (Two white houses now sit on top of this knoll.) The other possible location is the bluff between Porterstown and the Antietam upon which the residence of J. Eckers rested in 1862 and "Greenbriar Farm" sits today. "Map of the Battlefield of the Antietam," in George B. Davis et al., The Official Military Atlas of the Civil War (1891– 95; reprint, New York: Fairfax Press, 1983), plate 28, map 2. Both of these locations would have given McClellan a view of the northern part of the battlefield that was less obstructed by the East Woods than the Pry House and made it easier for him to communicate with Burnside. Strother's 1868 article is the only significant source that contradicts the traditional view that McClellan spent the entire Battle of Antietam, except for his afternoon visit to the East Woods to talk with Franklin and Sumner, at the Pry House, although there is also an account by a member of the Fifth Corps that recalls seeing McClellan on Eckers's Bluff during the battle. Thomas M. Anderson, "The Reserve at Antietam," in Battles and Leaders, ed. Johnson and Buel, 2: 656. Nonetheless, I have chosen to accept Strother's account of McClellan moving his command post. It seems logical that at a time when he had just ordered Sumner to join the battle and was contemplating sending orders to Burnside to commence his attack, McClellan would seek a vantage point that might give him a better view of the battle north of Sharpsburg and improve his ability to monitor operations south of town. It also seems unlikely that Strother would have made something like this up in an article that was certain to receive wide circulation at a time when there were dozens of people, including McClellan, who could have refuted it. To the best of my knowledge, no one ever did."
Rafuse, Ethan S. (2011-11-23). McClellan's War: The Failure of Moderation in the Struggle for the Union (p. 474). Indiana University Press. Kindle Edition.
Edit:
Let me point out that most people ultimately draw from Charles Coffin's description 24 years after the event. He indeed says the HQ was at "the large square Mansion of Mr Pry", but then describes it as amongst Porter's 5th Corps and describes the fields east of the Mumma and Roulette Houses as across the creek. Well okay, but that's the Ecker House he's just described.
The available sources are thus:
1. Mr Pry told Ben Lossing McClellan's HQ was his house, and that McClellan slept late, and had a good breakfast, not bothering to attend to the battle until after 0800 (
original source). Carman repeated the story. It's nonsense as Stother, Snell and others saw McClellan at different places earlier than this, and there are documentary orders given by McClellan before this (including McClellan's second, confirmatory, order to Sumner to attack timestamped 0720).
2. Stother's Diary says he found McClellan early in the morning giving orders at the Newcomer House (west of the creek over the Porter/ Middle bridge) and they set up their CP on a knoll east of the creek near there colocated with 5th Corps HQ.
3. Coffin's article in the Century says as above; he says it's the Pry House and then describes the Ecker House's location.
4. Thomas Anderson in the Century says McClellan's HQ was overlooking the middle bridge with Porter's 5th Corps HQ.
5. Schell (41 years after the event) said McClellan's HQ was a on bare hill with Porter beyond Pry's Farm coming from the direction of Keedyville.
So it's really not clear it was the Pry House (Sumner's HQ of the night of the 16th). Once we reject Pry's claims that are obviously partially incorrect and look at the described locations it's likely the Ecker House.