Hey, Noa! I helped design the new manuscript so I can help shed some light on parts of this. Not a developer so I can't really address technical issues like a slow word count, but let me see if I can help a bit~

1. Noted on the centering! I won't go too deep into why the offset situation ended up being the case, but it's safe to say that we're not done with the manuscript by any means. This is just a big step toward where we wanted it to go toward. We'll continue to adjust things based on user feedback and centering/giving a way to center the text document on the page is one of those things we'll be keeping our eyes on.
2. Allowing users to put the manuscript sidebar on the right was something we originally planned, but didn't quite have time for. I'll chat with the devs but I'm not sure when we'll work it in—but I know they'll want to add this setting when they can.
3. Can't comment on this one for reasons stated above.
4. I find the fact you liked the panel-based display really interesting. Most people we talked with were excited to lose that in this particular module. Sure, it's useful in Characters etc., but we found they mostly got in the way in the manuscript (especially in Explore). I'll keep an eye out to see how people feel about this as we move forward but based on my research and conversations with users while testing the design, it will probably stay this way. However if there's issues with your project theme that's a problem. One thing you may not have noticed is that right-clicking on the background will let you swamp between the flat background and whatever your theme uses—that may help. If you're seeing issues elsewhere let us know.

I hope this is at least helpful to know some of this is planned/we're watching to see how people react. Thanks so much for the feedback, and thanks for trying it out! :)