As he said, the Legionaries are nationalistic and view Malta as first priority. The fact nomads are known to use humans for their own goals is known and something the Legionaries wish to avoid. Same way they don't want to put outsiders in power because of fear said outsiders might use Malta and the Legion for their own goals.
As for Zoners - the Legion views Freeports as a place of potential staging of raids against Maltese space. It's in vanilla lore that the Freeport in Tau-37 is used by Bounty Hunters to hunt Outcasts. Also it could be added that in their own way Freeports claim clay space of their own that otherwise should be Maltese. Basically you filthy zoners are a necessity that we unfortunately don't really like.