I think flipping it back to 85mm wide 100mm tall is a big mistake. None of what he wrote is true, Q factor is pedal to pedal, and it will be at least 160mm anyway. So the downtube getting a bit wider won't be noticable at all.
This is my coaxial, 104mm box, I've never had the box touch me on accident, it is actually useful for extra control to squeeze between your legs for let's say a no hander. As your legs complete sort of a triangle from the seat down to the pedals, with the battery in the downtube there is no chance of interference.
You will have the chainring holder sticking out of the 105mm plane on one side, and the motor on the other. Shrinking it makes no sense, you won't be able to use that space anyway.
In addition, here the cells would be resting on their bottoms instead of each further row putting extra pressure on all rows below them, and the center of gravity would be lower, same with the visibility profile from the side.
The 48v idea is terrible, if you want 5kw, you would need 100a+ with 48v, while just 75a with 72v. Even at 72v it spins only 4500rpm.