The footnote you mention covers Miller's classification of 'militia weapon' as being one in where members of the disorganized militia "were expected to appear bearing arms supplied by themselves and of the kind in common (military) use at the time". You know, how the Miller court looked at Miller's short-barreled shotgun.
The operative argument you're missing is:
"... In that respect, Miller may be in tension with itself. There is no justification to limit the Second Amendment’s protection to arms that have military utility."
But yes, Heller is making the case that backpack nuclear weapons are "of the type that serve no ordinary civilian function".
I admit I read it with paranoia.
My G_D, who wouldn’t.