While you retain the mag capacity of an AR, you lose a great deal of a 5.56's effectiveness from a really short barrel:from around 3,082fps at 16" to about 2,172fps at 6". And of course, a bullet like a 5.56 NEEDS velocity to make it effective, as compared to, say, a .45ACP hollowpoint.
Combined with gunnutery's excellent point about noise and blast, (I'd be loathe to fire one without hearing protection ANYWHERE, much less in a closed room), and I think traditional handguns have an advantage that outweighs the mag capacity of a pistol AR.
Larry