Also, Lee was offered command of the Union army by Lincoln himself, so it's not like he'd be starting out low on the totem pole.
No he wasn't. Blair offered him the rank of Major-General in the Regular Army and command of the Washington defences. He was one of four chosen for the rank (Fremont, McClellan, Halleck and Lee), although Halleck took so long to get back from California that it is missed (was missed by me until my mistake was pointed out).
There were already two regular brigadiers (Wool and Harney), and Sumner was promoted BG March 1861. In May 1861 Mansfield, McDowell, Robert Anderson and Rosecrans were commission BG in the RA.
The assignments of the regular generals initially were:
Bvt Lt Gen Scott - commanding US Army
Maj Gen Fremont - Dept of the West (replacing Harney who was removed from active service after negotiating with Missouri)
Maj Gen McClellan - Dept of the Ohio
Brig Gen Wool - Dept of Virginia (i.e. Ft Monroe)
Brig Gen Sumner - Dept of the Pacific
Brig Gen Mansfield - Dept of Washington
Brig Gen McDowell - Army of NE Virginia
Brig Gen Anderson - Dept of Kentucky
Brig Gen Rosecrans - a brigade commander in McClellan's forces
Mansfield held the command offered to Lee. It is likely Lee would not have superceeded McDowell, but would have spent the war commanding the Washington garrison.