And I think the reason the edits feel to you like they cut in the middle of a scene, is because they do. This happens with the theatrical cut of every film. It's called editing. We just don't realize it because we haven't seen the entire scene, we see the parts the director wants us to see. You've watched the Star Wars saga a million times and you've gotten used to the flow of the George Lucas version. I don't think that fact can be used in criticism of ADigitalMan's editing skills or whether or not his edit of the film is good.
I went back and looked at the scene again. It's not as abrupt of a cut as I remembered it. My rational thought was that considering how into politics Padme was (she was questioning him about his views a few seconds earlier), she wouldn't let it stand and there'd be some attempt on her part to interrogate him further, etc. The cut just kinda left it too open.I also remember a much more awkward cut in this edit . It's the inclusion of the Padme's bedroom scene. Basically she's telling the story of the alien kids. It ends with her saying, "They all died" and then it immediately cuts to blaring triumphant music and Obi-Wan coming out of lightspeed. It just needed an extra beat in there. It needs more room to breathe. We're hearing a pretty emotional story and then suddenly it's forgotten about with a pretty upbeat music cue. I thought it was actually a fairly unintentionally funny moment. It reminds me of one of those "Walker, Texas Ranger" clips that Conan O'Brien used to have on his show. Basically, a very young Haley Joel Osment is talking to Wilford Brimley in good spirits explaining his nickname, saying stuff like "It means 'little friend' in Cherokee!" Very suddenly he looks up and says "Walker tells me I have AIDS." and the clip just cuts and the audience it left going "WHA?!"

Anyway, I just wanted to make it clear that I didn't bring this up to deride ADigitalMan's edit. It's a solid piece of work. It's my favorite fan edit of AOTC. There are just a few beats that felt off to me.