Darth Venal said:

And this logic you're going on about Dooku being a character of unknown affiliation... exactly how long do you think viewers were wondering which side he was on? If the script was trying to pull off some mystery about him then it fails completely. There's ambiguous dialogue with Obi-Wan after he sees Dooku colluding with the Seperatists which achieves nothing whatsoever because it's so badly written, then a scene or two later he's watching two Jedi and a Senator about to be slaughtered. Oh, and then he flees, fights three Jedi and escapes to be with his Sith master. At what fucking point are we supposed to be wondering whose side Dooku was on?

Give me a fucking break.

I don't think anyone here is under the impression that the film in its current form implies that Dooku's affiliations are unknown. We're talking in respect to edits, where he is made a rogue Jedi who is the only one who knows that the republic is being controlled by the very evil they want to destroy.

The scene with him reporting to Sidious would be removed in such edits, and the other scenes you mention, tinkered with.