I'm amazed how much of editing he actually does by hand (like growing/shrinking indentation) and mouse. That sort of switching between actual coding and lexical editing would kill my flow.
If you're noticing the same thing I did, he's doing that because he's working on OpenGL shader code that's embedded in a string inside his Dart code. In this case, the IDE only sees a plain vanilla string, so Notch has to indent the GLSL manually.
I'm watching now and it doesn't seem that bad, sure he switches tabs with the mouse but it seems like he is using quite a lot of keyboard shortcuts otherwise. I'd almost wager he has a plugin to emulate vim or emacs keybinds, seeing as he's moving the cursor forward by words and jumping around the code a lot without using the mouse at all.
I come from windows and now use a Mac (iOS dev). I was so used to all windows shortcuts (shift+ctrl+keyright to select a word, ctrl+c to copy, etc), I know what you mean!
I use KeyRemap4MacBook, which kicks in as soon as I connect my hardware windows keyboard to it (which is basically always when I sit down to code). It has a lot of default windows compatibility settings, but you can customize at will. I added a few myself by hand as well (also to get desktop switching the same as I was used to from Ubuntu :).
My flow has always been a mixture of keyboard and mouse. Even as far back as RHIDE with DJGPP. I basically program with 90% thought, 10% code. So a faster interface doesn't change much for me.