Here's a thought: what if a Free or Chartist Captain decides that he's bored of trudging slowly between two tedious star systems under the restrictive terms of his charter, and opts to leap his ship and crew into the warp, travel to the Koronus expanse, and start trading within it?
He would lack a warrant of trade, so would be forbidden from returning to the Imperium and trading there, but we've seen that there are still plenty of places within the Koronus Expanse that are happy to trade with anyone: Footfall for example.
It would of course be a huge risk for a free captain, as he'd be prey to pirates, travelling without a dynastic support network etc...but are these risks really much greater than those of a "proper" rogue trader operating under a warrant?
I mean there are many obstacles to this course of action: not all free captains have navigators (many make dozens of short warp "hops" instead), you'd become a wanted criminal, and there's the thorny issue of what your crew think about all this... But none of these obstacles seem completely insurmountable to someone with limitless ambition.
A "true" Rogue Trader like this (ie one who's truly operating completely illegally) might make for an interesting NPC for players to encounter...