Actually the Miller court said that military firearms were protected by the 2A but they weren't shown any evidence that a short barreled shotgun was a military arm that would be protected. Of course they were but as you mentioned no one was present to represent Miller as he was dead.
That decision has been misread and twisted by gun grabbing judges and lawyers ever since.
The Miller decision also ignored the prosecutions claim that Miller was not protected because he wasn’t a member of a Militia. If Militia membership had been a requirement then the nature of the weapon would have been irrelevant. Instead the case was remanded back to the District Court with the guidance to examine the weapon, but Miller himself would be protected if the weapon was useful to a Militia.