When I run this on my shaman it includes a bunch of deity-restricted spells that I can't memorize (hence, are not missing). Example: I worship The Tribunal. "Greater Mass Imbue Amber" shows up in my missing spells output, but that's not missing for me because it's only for shamans who worship Cazic-Thule.
Been like that since the start. Clerics have it worse, but all classes with deity restricted spells have to learn what to ignore. I asked the question during a developer Beta raid one year and they said that it would require a rewrite of the /output missingspells system (partly the dev thought because deity can be changed on a character through the race change scroll). It would be nice(tm), but there are literally 100s of things that I'd personally want first and except for this fact (and a few errors in a couple of classes for spells that show that should not), this actually just works.