I think the reasonable decision would be to establish three single-member seat constituencies in the northern territories. I think these people would become frustrated with the others, which would have the possibility of having several MPs. After two or three elections, they would ask to be grouped together to establish a single constituency with three seats.
In any event, the fact remains that three single-member seat constituencies would have little impact on the balance of political parties in the rest of the country. The fact that three out of 338 constituencies don't obey the same rules as the others cannot create an imbalance in the system. However, it may influence the choice that these people will eventually want to make.