The legal answer: it’s a criminal offense under NT bye-laws to disturb, interrupt or annoy anyone using NT property; other than that there is no law whatsoever to prevent you taking off elsewhere and flying over their land; if you take off from their land they could (at most) declare you a trespasser and ask you to leave. So: get out there, get on with it, and do what you can to avoid disturbing anybody.
If it helps give reassurance, these photos and this pano were taken while flying above NT land (and indeed, standing on it, although I only found that out afterwards).