I haven't read Ms Young's work and cannot comment on her case against the 21st Georgia specifically.
Throughout the fall and winter of 1861-2, the search for and seizure of such souvenirs as Ballou's skull was widespread among the Confederate troops encamped around Centreville and Manassas. Members of all four of the regiments that I am researching (2, 15, 17 Ga in Toombs's bde, 20 Ga then in Early's) complained of comrades within their units, along with soldiers in other commands, disturbing and taking the remains of fallen northern soldiers. "Complained" isn't the best word, as many mentioned it to family and sweethearts, sometimes in a manner that suggested they were fulfilling requests from home for hair, teeth, clothing remnants & c. Some soldiers in each unit were repulsed by the practive, some soldiers in each unit gladly participated.
Local entreprenuers - black and white - even got into the act, selling bones to soldiers when their units marched off, and the men hadn't finished "shopping" for their friends and families. I get the sense that most of the small items were sent home almost immediately. Northern troops occupying these same Confederate camps in March of 1862 noted macabre decorations on the outside of some of the huts used by Confederate soldiers - namely, real skulls and crossbones.
Men from virtually every Confederate unit in the area did this sort of thing. Unless there are some really good primary sources (and maybe they are present in Ms Young's book?) tracking Ballou's skull, it could have wound up anywhere.