Zen of No Zen.

Nothing is really hidden, there are just things that are not really explained well enough to gain any sort of understanding.

** A Punch can be a reach out and grab, or it can also be a punch.
** Chamber can be a pulling motion, or it can be a strike to the rear.

Even this view is limited by the fact that it is either/or, but it can be both, it can also be neither.
It is what it is, and the first thing that needs to change is the practitioner's mental approach. What is in your mind when you practice? More often than not we do not question explanations, and sometimes there are no explanations given.
Explanations themselves are easy to relate, but when someone takes an explanation as gospel they fall victim to an idea that spreads like a virus and serves only as a divisive force between them and the bigger picture.

I have a saying that applies here just as well as anywhere else, 'I do not like isms, they give me a rash.'
Style is just as much an 'ism' as Buddhism, or anything else. This is not Church and we are not in some Kung Fu movie taking place in a mysterious Temple atop a mountain.
You cannot stop punches with your mind, or catch bullets with your teeth. A punch is not necessarily a punch, but at the same time it is.

** Karateka throws a punch, I block and counter with a reverse punch (breaking into two movements even at the level of brown or black belt).

We have surrendered to the notion that this is how things happen, at each level we don't ever move beyond this; at least this is the way we tend to find it in most Dojo throughout the world.
There is etiquette, there is a specific mentality, there is propriety and all sorts of other things that literally have nothing to do with anything. Am I saying these are bad qualities? No. Am I saying that we should do away with them? No.
What I am saying is that we need to look a little deeper, a little closer, with a mind that is free to move about and explore, not attached to anything specifically, but definitely questioning what is going on.

Test things out, see what works in what type of situation. Rory Miller has some great material on this that will shed some light on strengths and shortcomings - break it down, rip it apart, nothing is sacred save for what works.

** Try grab and punch or some other combination/chaining movement when you're sucker punched from behind (taken by complete surprise).

1) How can this be changed, or discarded.
2) If discarded, what will work effectively in its' place?

Take a look at things from these differing angles, include pre-emptive action, include situations of surprise attack/ambush, include multiple assailants, include assailants both with and without various types of weapons.
Get into the mindset that what doesn't work, if used in these situations, WILL end very poorly for you... Death, dismemberment, ect.
Don't get stuck on what something means, some specific interpretation. These things don't really matter, those things are meant to instill an understanding of fundamentals to help you along, they are not the end, but the means, and they are good to practice - Don't get stuck on them.

Even still, don't stop there, take it up a notch. So you're not used to getting hit? Most Budoka are not, and when they take a hit they tend to be surprised.
Get over it! Practice taking a hit. Get used to taking a hit. Even if it means bruising your pretty little face.
Budo may have safety measures built in so that we can keep training without serious injury, but it is most certainly not about playing it safe. At least not as far as getting in the right frame of mind goes.

Mentality is just as important as Physicality, and Physicality itself is not a determining factor.
Most are not athletes, certainly one could strive for better physical condition, but things tend to happen when you are least prepared for them; the mind, therefor, needs to be right - everything else is subordinate.