There are good reasons for leaving it in and good reasons for taking it out, and even I don’t know for sure where I stand. For me, the best reason to remove the droid factory sequence is because doing do actually heightens the tension of the following scene where Padme sits down with Dooku. Padme at least appears like she’s going in there with a degree of influence and clout, rather than as someone who is already a hostage. There is at least the pretense of a real negotiation about to take place, and they only realize by the meeting’s end that they are completely screwed.