Everything I've found suggests that the lands conquered by the Order were sanctioned by the HRE. How does that not make them 'part of' the empire, if at least only nominally? Those lands occupied by the Order which were de jure part of the Kingdom of Poland I can see being exempted, but why not the rest of the Order-State?
Because this isn't what happened? Here's Norman Davies' slant on it in
Vanished Kingdoms:
"In 1226, the emperor's Golden Bull of Rimini stated that thduke of Mazovia should equip the Order to fight the pagans, and that the conquered territory should be Reichsfrei, that is, beyond imperial jurisdiction . . . . In 123, the self-contradictory Golden Bull of Rieti of Pope Gregory IX . . . subject[ed] the Order exclusively to papal authority."
Danzig and surrounding Pomerelia had been part of the HRE before it was taken over by the Order---why would it cease to be so?
Why do you think Pomerelia was Imperial, as opposed to Polish or Danish? Boleslow III doesn't sound like a German name, and he was a ruler in the region.
And again; where are the representatives of Riga in the Diet? The evidence that the Imperial courts were the last court of appeal in the region? The signs of, err, Imperial governance? To make the territory Imperial, you need something more than the document from some watery tart.
Sovereignty in the area was not black and white in OTL, and not helped by the fact that the Empire was a joke.