You made so many changes to the MM clone dough formulation that you referenced that it becomes very difficult to do a proper diagnosis and render a useful prognosis. However, I will try to walk through all of the changes you made and offer my comments.
To begin, I do not think that using the Newcastle Brown Ale was a problem. However, when you used 12% Newcastle Brown Ale with 38% water, to equal the 50% formula hydration in the recipe you used, you should have made an adjustment to the total hydration to reflect the fact that ales, like beer, are not all water. About 90% is water. So, adding about 10% more solids to the recipe without adjusting the formula hydration would have made for a lower hydration dough. The final value would be increased to reflect the water content of the molasses and the addition of the oil, but the total may still have been to low to perform optimally, including getting a good oven spring. The latter was also not helped when you decided to use a pan instead of a pizza stone. The reason is that before the dough for the pizza can start to bake and to rise, the pan itself has to get up to the proper bake temperature. Depending on the type of pan and its characteristics, including type of metal and its thickness, that can take some time. At the same time as that is occurring, the top of the pizza is getting top heat to start to bake the pizza. Without sufficient bottom heat, it would be difficult to get an optimum oven spring. As Norma noted, you perhaps should have let the dough ball rise longer rather than forming a skin and letting it rise in the pan. That step, perhaps along with others that you used that were out of the norm for an MM clone pizza, may have been responsible for the texture of the crust and crumb that you experienced.
Finally, the use of a conveyor oven to bake a pizza that is intended to be baked in a deck oven, introduces its own set of problems since it is hard to get a hearth type bake using a conveyor oven instead of a deck oven. What some pizza operators do is to use special cloud type disks (such as sold by PizzaTools and shown at http://www.lloydpans.com/standard-pans/pizza-tools/quik-disks/hearth-bake-disks
) to get a hearth type bake out of a conveyor oven. It may also be possible to use a special pan such as shown at http://www.lloydpans.com/standard-pans/pizza-tools/deep-dish-pans/deep-dish-thick-crust
In order to do what you are attempting to do will require a material change in the MM clone dough formulation you used and quite likely the bake protocol also. Should you decide to proceed along those lines, you might want to start a new thread so as not to steer this one in a new direction. Even then, you may want to use an approach that changes only one variable at a time, whether it is in the dough formulation you decide to use or in the bake protocol.
BTW, the All Trumps flour has a protein content of 14.2%. We don't know for sure what the protein content is for the flour that MM uses but I do not think that using the All Trumps should have been a problem.