I can’t see any way to make a complete removal of the factory scene feel seamless. A Dooku VO would not be enough, a real version of the movie just wouldn’t handle the transition that way. It would establish Dooku finding out about Anakin and Padme, and then it would show Anakin and Padme being apprehended and taken to Dooku. Unless there are deleted scenes somewhere that show this, it just won’t feel like an official edit if we jump straight to Padme talking with Dooku.
Honestly, I think the rest of this edit improves AotC so drastically that it can afford to have a single, trimmed down less-than-stellar scene for the sake of feeling like an official movie edit.
I mean, to be fair, Padme said that she wanted a diplomatic solution to the situation. Therefore, it makes sense that they could simply walk in to talk with Dooku without any real confrontation. The reason Obi-Wan was apprehended was because he was sneaking around and sending messages via his ship.
Why wouldn’t they just come in the front entrance then? I think the preceding scene implies that they are looking for an discreet entrance to sneak in.