I agree if the rules use the same ruleset then you're really talking about the same game with a new campaign idea.
Frankly, paying for the rules twice just so it can be sold as a stand alone game doesn't appeal to me.
I'd rather have one rulebook with all the rules and have each incarnation being built off of it.
It ticked me off with White Wolf's game systems and it will tick me off with this one as well if they head down that route.
Still going to buy it, but my grumblings will continue.
Remember though, FFG took over this game from BI. I hear what you're saying though.
Optimally you'd have:
WH40kRPG Main Rulebook>Dark Heresy (Campaign Setting), Rogue Trader (Campaign Setting), Creatures Anathema, DeathWatch(Campaign Setting)
Naturally, if you want to play RT and have no interest in DH, then you buy the Main Rulebook and RT. Unfortunately, FFG is in the position that they have to tell RT players they have to buy DH (because it's the "main rulebook") OR rewrite/reprint the core rules in RT.
They could write and print a new Core Rulebook, but that's a gamble as most of the existing players might not buy it because its already in DH.
Another alternative is they distribute the Core Rules with no campaign fluff online as a free .pdf download. That way, they could put more crunchy stuff in RT, satisfy the RT-only players and make the DH players happier and feel like they got more for their money when they buy RT.
But of course, they're probably going to just reprint the core rules in RT. This is going to be a big problem if they feel the need to continually reprint equipment lists, etc. At some point, the logical thing to do would be for them to say "Yes, RT, DW and DH are the same game and the upcoming Xenos Lover's Compendium is intended for use with all three..."