Actually, reading Andy Abbott's book, Rossi says he's constantly talking to himself on the track...telling himself to brake earlier, get on the throttle sooner, etc. I think the difference is that he's really not THAT far off to begin with...but he still has the awareness to know what could be better.
I am most certainly a Johnny-come-lately Rossi fan, as I only got into this sport two years ago...but I'm just in awe every time I watch him race ...even when he's not having the best of days.
Thinking about how to change your reference points/racing line is different than paying attention to how to ride the motorcycle itself. I think SRs are usually caused by there being an overwhelming number of things (could only 2 different things before it becomes overwhelming) that a rider might need to deal with which causes them to freeze up or make mistakes. This isn't something Rossi needs to worry about which lets him be much more aggressive and comfortable with changing up racing lines to get faster or to make a pass.
If your going to change your line its going to require some thought. The less you need to think about how to change your line (control the bike to get there) the more you can focus on simply which line you want to ride. Most riders need to think about how to put the bike where they want it, professional riders only need to think about where they want it and not how to get it there.
I would think braking too early is a result of SR's (which, now that I have the book in front of me, I can confirm is what he was talking about). Personally, I don't believe SR's ever go away...simply because its not a controlled reaction. Sure, these guys have pushed them well beyond anything most people could ever dream of, but they are still human...and when pushed beyond their comfort zone they will ignite those SRs. Now, don't get me wrong...in many cases their SR's aren't triggered until the bike itself actually can't handle the situation...but not all...particularly during a race. Just an opinion though...only those gods of motorcycle riding truly know whats going on in their heads.