I know it's not directly what you asked for, but Stars Without Number is a fantastic Sci-Fi RPG, and is super open like Rogue Trader was. Honestly, reading it reminded me of when I first read Rogue Trader as a kid.
The single worst thing about it is that the cover of the book doesn't look very exciting when compared to other RPGs.
FWIW, you could easily map the lore of 40k (either the fun RT lore, or the modern stuff) onto the SWN game system without breaking anything.
Why would you want to use a different system than the original RT? Let's just say that in the 30-odd years since RT came out, much better game mechanics have been developed.