Well, my answer on the changing exercises will be different than most.
Changing exercises all the time is popular with many. There are reasons other than gains that it is a terrific thing for the bottom line of trainers/coaches, and reasons other than gains why it has a great appeal for many lifters.
There are also good reasons to do it, including:
1) The exercise was added to correct a specific weakness which has now been taken care of, or another need has now become more important and it is better to devote the effort to this new need
2) A better way to accomplish the same purpose has now been found
3) The exercise had been suited to the parameters the program was aimed to meet before, but due to periodization or other reasons what one is trying to achieve is now different, and the exercise isn't suitable for the new parameters.
That may not make so much sense, so as an example, perhaps one had been in a phase of doing higher reps with lower percent 1RM and now is moving into a low reps, high percent 1RM phase. And the exercise is one which works well for the individual with light weight and high reps but not at low reps. So changing it out makes sense.
4) Due to other changes for other reasons, the exercise is now unneeded or duplicative or there is some kind of conflict. For example, let's say one decided to increase volume of standard squats by quite a bit. Another type of squat that was being done might be taken out. Or let's say that squatting was being done twice per week but due to other changes the lower back is now being very heavily worked and the second squat workout is being compromised by the back not being enough recovered. Squats in that second workout might be swapped out for hack squats or leg press, for example.
5) Because of injury or developing problem, or experience that a given exercise gives problems if done every single week. For example, someone might tend to develop shoulder problems if flat benching every single week of the year, but does like the exercise, and therefore has periods of the year where he flat benches and other periods where he does not.
Or other reasons like these.
But not simply because 3 or 6 weeks have gone by or whatever.
Now, some like to change exercises for no reason other than that, or "because I couldn't add weight or reps this week and so that means time to change exercises so I can give myself the illusion of constantly getting several percent stronger every single week!"
Anyway, no, I don't think you need to swap exercises during a 12 week period on account of getting stale. Varying rep range and weights, or otherwise varying protocols will address that.
Those well adapted to ketogenic diets and adapted to volume such as you've outlined could do fine on it. Someone who had never done volume like this and had never done ketogenic dieting would quite likely find this to be overdoing it.
I really don't know about energy systems work.