During the last 120 years wheat was optimized for machines making its gluten content higher that could explain higher gluten intolerance among people presently.

Is there any evidence supporting this hypothesis?

For context: the molecular shape of gluten causes dough to hold better. Wheat with more gluten gives softer bread which rises better. Hence why gluten is so prevalent in domesticated wheat.

We’ve been optimizing stuff for palatability and processing since we started domesticating wheat. I am going to need a better argument about why gluten is special.

The article does not support your hypothesis. Celiac disease is not 'gluten intolerance'.

Asking out of ignorance here: why is higher gluten wheat more optimal for machines?

Main role of gluten in bread is to keep gas, usually CO_2 from yeasts, bacteria or baking powder, inside dough - so dought raises and when heated gas expands giving even more volume to (not only) bakery products.

Gluten do this by forming gluten net during dought mixing. Or even by mixing flour with water and waiting. So gluten is super good and almoust magical ingradient.

Real problem is that Western World started to abuse wheat flour after yeasts were discovered. You know, in older times "white bread" was mainly for rich peoples and poor peoples used flour with more chaff. But in last years chaff costs almoust same as flour :)

Celiac disease is only 1-2% population, and non-celiac gluten sensitivity is 5-6%. So that "harmful gluten" is a myth. But if you have some intolerance then gluten is very very toxic. And nothing wrong with skipping it. https://en.wikipedia.org/wiki/Gluten

Rye flour contains some form of gluten but it do not form gluten net. But still can be toxic for ill peoples.

So, using wheat flour/gluten is simplest way to have bread that have nice volume. Other flours are good for pies or require to use cake mold.

As for why gluten is better for machines: when dought contain formed gluten net it make it elastic, a bit like gum. So it can be nicely formed. Dought also can be to strong with too much gluten - that require much more force for shaping.

Also with good gluten net dought can sustain longer period after forming and before baking, making it less time sensitive - bread do not get flat before there is free place in the stove/oven.

It was not done on purpose. As an unintended consequence of selection for easy to harvest mechanically, easier to bake, better to respond to fertilizers modern wheat varieties contain more specific proteins of gluten type that cause allergic reactions.