As far I understand (as a youngster) few squads of Space Marine can be provided to a Rogue Trader to perform a specific mission for the benefit of the imperial autorithies in outer fringes (the said mission can of course last decades...). I'd rather see this as a Rogue Trader - Space Marine joint operation under Rogue Trader leadership.
I can't imagine (under normal circumstances) Space Marines (not to say a chapter) to be permanently attached to a RT. I mean there is no Chapter based in Calixis Sector, just few marines for ceremonial purposes (plus I guess few squads of deathwatch but there are out of range of a RT).