I have recently been reading through Stars of Inequity and I greatly like the system and planet generators. However, when I get to colonies I am a little confused. So my question is; Can a Rogue Trader establish a single colony per planet, or per territory on a planet?

The upper sizes of a colony are 'City', 'Metropolis' and 'Hive', which leads me to think that it doesn't so much as occupy a territory, though I would limit each planetary territory to one colony only, unless you are playing a game centered entirely upon the one planet or system.

Yes, 'Territory' is listed as a size but it is smaller than 'City' so I am certain a Territory-sized colony is not the same thing as a planetary territory.