Most of this, I believe, is fairly easy to understand, based upon what I know about the brain. I think that the feelings and problems that have been outlined can be explained with less difficulty than is supposed. Since I am not a neuroscientist this will not be a great answer, but I believe what I say will shed light on the subject.
Covering our brains is a thin sheet called the neocortex. If you look at a top down view of the brain and see all those nice folds, you are looking at the neocortex. It is very thin, but it is the part of the brain that contains the part of you that understands what I am saying. It is there that knowledge of self is held.
Many of our sensory inputs and motor outputs have connections in the neocortex. There are defined pathways that most sensory input follows to the neocortex. However, there are smaller bandwidth pathways that take different routes, and I can't recall off the top of my head what portion of the brain they are routed to, but those parts of the brain watch for certain patterns and fire off immediate emergency "subroutines" when one of those patterns comes in. When you react "without thinking" to a sudden frightening stimulus you can thank these pathways for that quick response. If the logical mind had to decide what to do most of us would probably be dead already. I know with certainty that I would be. I took a lot of dumb risks as a teenager and my "reflex" responses saved my life more than once.
The logical part of the mind can view these responses as being separate from itself because they are. But they still take place in the brain and are a part of you. Nobody ever wonders who's breathing for them or who's making their heart beat. You don't say you have a split personality because some functions are autonomous, it's something you accept because it has occurred your entire life. These other situations are similar, we just aren't used to them, so we can feel disconnected from what is happening.
I don't know what it is called now, but kinesthetic memory is what we think of as muscle memory. You perform some task over and over again and your body becomes so used to doing it that you no longer have to think about it. When I learned karate this is one of the main focuses of the training. When you are fighting for your life you must react without contemplation. (I should point out that it isn't your muscles that are learning it, although they may develop an increased ability to do what you are training for, what is really happening is your brain is wiring for those motions).
When you first learn to drive you pay attention to every detail of what you are doing, and most people do a very poor job of operating a car. After much practice we become so good at it that we can let the part of our brain that learned it take over and do it. Learning to type is similar. But after you've become a good driver, you can literally drive a hundred miles or more thinking about something else and somehow manage to not kill yourself and everyone else. This is one of the wonderful features of the brain. When learning, we have to focus, when we have learned, we can use "auto-pilot". There is a term for auto-pilot but I don't recall that either.
To sum up the point I am trying to make, when we learn a new skill we do not add a new gremlin to our brains, we enhance our whole self.
It is only when an aberration occurs that we develop problems with the harmony of our brains behavior.