According to Jackson's report, no. Only Jackson's division (J.R. Jones), Ewell's division (Lawton), and A.P. Hill's Light Division were part of his command.
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The common but incorrect assumption about the order of battle for the Army of Northern Virginia comes from confusion resulting from the organization of the First and Second Corps, which happened in the campaign after Antietam. After the war, many people just assumed that the divisions fought under Longstreet and Jackson because Longstreet and Jackson were the two corps commanders appointed after the battle. While Longstreet and Jackson were the primary wing commanders, Joseph Harsh argues that D.H. Hill and McLaws temporarily operated as "wing" commanders (though with less permanence than the forces attached to Longstreet and Jackson) because Lee was testing potential commanders for a third maneuver element, with Hill in particular in place of G.W. Smith, while D. Scott Hartwig argues that the divisions outside of Longstreet and Jackson were just independent of the wings and assigned as needed.
Per Hartwig, the Army of Northern Virginia was organized at Antietam like:
Longstreet's Command
D.R. Jones's Division
Hood's Division
Evans's Independent Brigade
Anderson's Division
Washington Artillery
S.D. Lee's Artillery
Jackson's Command
Jackson's Division
Ewell's Division
Light Division
Independent Commands:
D.H. Hill's Division
McLaws's Division
Walker's Division
Reserve Artillery
Stuart's Cavalry Division
For most of the campaign, D.H. Hill's division, McLaws's division, Walker's division, the Reserve Artillery, and the Cavalry Division all reported directly to Lee. This is why D.H. Hill is receiving an order directly from Lee's headquarters. In the normal military protocol, if he were part of Jackson's command then the order would have gone through Jackson. Jackson, who thought D.H. Hill's division was still under his command, followed that procedure, unaware that Lee was sending a direct order.