I don't know, it seemed pretty obvious to me that Dooku calls her his "apprentice" to appease Assajj's desire to serve them... I mean, if he said, "You did well, my pawn who I'll probably have killed off at some point", would she be so willing to serve?
See, it all plays into her character too, in that she's very gung-ho and eager to become Sith. She truly doesn't understand what it is to be Sith though... That's kept from her. She's Dooku's apprentice, so long as it serves Dooku's purposes. She clearly doesn't seem versed in the ways of the Sith as her masters are. Again, she's just a pawn.
She's often referred to by others as an "assassin" as well... Not even too Sithy it seems.
I think all the EU jives then for the most part... She turns up super early in the Clone Wars, possibly even having been recruited prior to their start, and she keeps turning up to do the dirty work Dooku and Sidious just simply don't want to do, like harassing Jedi. Sidious even seems to be using her in a manipulative way against Skywalker, possibly (likely?) without Dooku having a clue about it.
To me that all jives then... I don't see a need to have something go back and "make it fit" because I can't see the actual break in her character at all.
And yes, Tol Skorr! I forgot that dude's name, but he's a total puss by comparison. Maybe h's just not reliable? That's why Ventress gets most of the work? When's he eventually even die?
Can't wait for Season 3. Love new CW toons to watch.