The 5.56 does not stabilize for a distance out of the barrel. During this unstabilized flight, the bullet will apparently upset and not overpenetrate bodies and/or other objects struck. After the bullet stabilizes, however, it will drill a nice hole in all sorts of things. I have no personal experience with this, but I do recall speaking with a member of a local SWAT team who shot a pit bull at close range with a M4 and the bullet stayed in the dog.
Back to the OP, advantages of a shotgun over a subgun for entries can depend on the ammo. With buckshot, you can put 9-12 pellets (and wound channels) on target at one time out to moderate ranges, which is hard to do with even a good subgun like an HK. All subguns climb, so unless you are really close, you are limited to bursts of 3-4 shots to keep on target, as opposed to the shotgun which delivers all pellets with one recoil impulse. With slug loads, you can penetrate most soft body armor at moderate ranges, which a subgun will not do (I know it gets bantered around that slugs won't go through the vest and will injure through blunt trauma, but I have seen a vest, IIA or III, penetrated through both sides in a test by a local PD).
Subguns, however can go from a multi-round weapon to a precision weapon out to moderate distances simply by going to semi-auto, and the ones that fire from a closed bolt are usually very accurate, with obvious SWAT applications. Tough to trust a close head shot to a shotgun.