Scale this up to the size of the universe and instead of using binary use a multidmensional whatever as a calculation substrate and the univese is just a giant computer using electrons and nuclear forces to calculate out an answer in EXACTLY the same manner as the wooden machine in the video.
Well, that wooden contraption is a fair representation of how an ALU in a computer's CPU works when it needs to add two numbers. Of course computers these days can do more than simple addition, but that is the start of them. Add an understanding of 2s complement and you can do subtraction as well, repeat and you're doing integer multiplication. Division is hard to do electrically, and tends to require a recipe of operations and conditional loops to do right; even the early ARM chips could do addition, subtraction and multiplication but didn't provide an electrical solution to division.
So, can you EVEN IMAGINE what it would mean for a universe to exist THAT DOES NOT DO CALCULATION AT THE UNIVERSAL SCALE?
Sure. Up until about 1950 you only really needed to emulate the earth and any other occupied planets. Everything can be hard coded for the time being. As I said at the beginning of this discussion, since then they must have had to pause the simulation and upgrade the computer repeatedly to cope with what we're doing, which is an argument against simulation.
What could it possibly mean for a universe to exist THAT DOES NOT HAVE DETERMINISM as part of the design, which is required for calculation?
The universe as it exists already doesn't expose determinism in all situations. It's been a few years since I read Brian Greene's Fabric of the Cosmos, but it documents a situation according to general relativity only I think of passengers on a train accelerating near light speed, where one shoots the other, but if you were to observe it from a train heading in the opposite direction, you'd see the second passenger being shot before the gun is fired.
Does the idea of free will even mean anything at all given the above questions?
Yes, free will is a tricky conundrum, but if you look at it from outside of the box so to speak, but all we can see outside of the box really is probability; most of the time someone will do one thing, but occasionally they'll do another. And really, quantum mechanics depends a lot on probabilities, so in that sense it could just be the exposition of quantum effects.
If the universe is a giant calculator, what was gods question?
According to Douglas Adams the Earth was created to answer the cosmic question of 'what do you mean, 42?'. Although now I say that I can't quite remember how the dolphins and the lab mice relate to that question. I think the question was raised by the Magritheans, famed for their design work on the fjords.
EDIT: Apologies about the last deepity. I thought it was funny.
Me too