Pythonic, the pictures of your pizza looked absolutely delicious and I would have loved to dive into a piece of two of it. A little "flaky" is often thought of as highly desirable, but too crumbly probably would not. I've never made one that was crumbly as you described and as one or two photos seem to show. And it should not tend to fall apart a little as you described. In any event, your pizza stilled looked great. I love that texture in a way.
Let me think out loud a bit regarding the crumble question. It could be because it is too dry with either not enough water or oil. It could be because of too high a protein flour (which would absorb the hydration more and make it drier). It possibly could be that it was not mixed enough and too much flour remained unincorporated (even tho the "mixing" time should be short, like just 30 or 60 seconds). Hope it wasn't too much bench flour. Melted butter? Probably not, as it adds some water to the mixture. I'm finding using very softened butter added at the last point with just slightly incorporating the butter really does a nice job, but melted is fine, too. (I know Malnati's uses melted, but in the home oven environment we have to do things a little differently).
My target for semolina is 20% but so many have reported back to me that they love a level of from 25 to 50%. If your brand or bag of semolina is too coarse you may want to try putting some through the food processor a bit to make it a little more finer, but usually most brands are good as is. And I trust you let the dough get up to room temperature after taking it out of the refrigerator.
The top rim of the crust usually does shrink down a bit during its bake, so I most often try to make the crust edge crimped as high as I can in the pan (even to the top). And even increase the recipe a little -- sometimes adding a 5 or 6% bowl residue factor so I have enough dough to tightly "press, crimp and pinch" the dough up the sides of the pan. BTW, your pictures showed that you did an outstanding job on crimping the edge of the pizza against the sides of the pan. That's the way true Chicago Style Deep Dish Pizza is meant to be. And it does taste much better that way.
The cheeses that you used sounded very good. I would guess around 10 or 11 ounces for a 9" pizza is about right, but others like more or less. And of the several groups of taste testers that I have, about half love a lot of crushed tomatoes and the other half would prefer a lesser amount, so it depends so much on preference. Of the incredibly large number of times that I've eaten at Malnati's home restaurant there in Lincolnwood, they always have a large amount of their great crushed tomatoes on top of their delicious pizzas. Some of their other restaurants, however, do things a little differently. I still have several cans of those great Malnati's tomatoes and consider them, too, to be among the best in the business.
Again, I am just super impressed with your pictures and can't help but believe it tasted every bit as good as it looks. Thanks for sharing your experience and pizza success with us.
Edit - Just had an after thought. Are you proportionately calculating separately with the pizza calculation tool the amount of AP flour and the semolina flour? You should not use the semolina ingredient space in the deep-dish pizza dough calculator, but instead just calculate the proportions of the flour ingredient.