Is there a point in mixing dough (let's say just flour and water to keep it simplest) where mixing/kneading/disturbing denatures the gluten that was developed? If so, what happens? 

I'm not sure I'm completely clear on the question, but I'll do my best to explain how gluten develops. 

Simple Answer: Yes, mixing dough creates a gluten network much more quickly than leaving the flour and water to sit, though some gluten will develop even there. Water molecules move at an average speed of about 1400 miles per hour at room temperature, so they're constantly crashing into each other and into other molecules, and that chaotic molecular movement drives a lot of chemical reactions. 

Technical Answer: Gluten is a mixture of water and two protein precursors found in wheat flour (and technically only in wheat flour; other flours may have similar molecules and produce similar substances, but it's not gluten). When the water and these two proteins (glutenin and gliadin) combine, covalent bonds called disulfide bonds connect the glutenin molecules into much larger molecules. At the same time, weaker bonds (hydrogen bonds) loosely connect the water, the gliadin molecules, and the glutenin networks together. All of these bonds are important. The glutenin network is what gives dough its strength and elasticity, and the hydrogen bonds in the gliadin and water molecules are what gives dough its extensibility. 

The strong disulfide bonds that connect glutenin proteins together are formed when the cysteine amino acids (one in twenty different amino acids that make up all proteins) get close together in water and a chemical reaction occurs that links them together. The cysteine amino acids have to be very close for this to happen. If you pour water over dry flour, a few of these reactions will happen, but they will only happen where the flour is hydrated (is mixed with water) and they will only happen when the cysteine residues (another name for amino acid) are very close together.

When you knead dough you are evenly hydrated the flour and you are also moving things around so the cysteine residues have a good chance of being near to another one they can bond with. The more you knead the dough the more of these bonds will happen.

When you mix dough and then allow it to ferment (assuming there is yeast mixed in), the bubbling of the CO2 through the dough slowly moves the molecules around, and that can also, over time, create a lot more disulfide bonds. Once these bonds are formed they are difficult to break. There are endogenous enzymes in the flour (proteases) that will cut these large proteins (the mesh network of glutenin molecules) into smaller pieces, which is why dough you ferment for several days will lose strength.

Another thing that is important is that when you rest dough (say, for 30 minutes), the bonds will rearrange themselves naturally into a more "comfortable" network that isn't so tight. That's why the dough is so much easier to work with after resting. 

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Please let me know if this all makes sense (you may want to watch the molecules lecture first) and if you have any questions. 

Molecules Lecture: https://chefsvillage.org/food-molecules-lecture/  

Chef Michael