RE, commercial cheese can be a little more forgiving, but, when it comes to supermarket brick, there's no way to judge it fairly unless you dial in the right thickness factor. Without a thin undercrust, not enough heat rises up to the cheese, so, rather than cooking from below, bubbling and giving off it's flavor, it cooks from above, browning a bit, but not really bubbling, and ended up bland, and in extreme cases, tough.
Marlon's WFO NY-style pie
thickness factor is where the cheese melting magic begins to happen. His more recent pies get a massive cheese melting assist from the fat from the pepperoni, but if you look at the first plain cheese pie in the threadhttp://www.pizzamaking.com/forum/index.php/topic,19065.msg186220.html#msg186220
you'll see exactly what properly melted cheese should look like. It's a bit clear/translucent and has craters and ridges from being bubbled. The cheese itself is a uniformly tan shade, but you don't really see much in the way of isolated browning. Unless you can achieve this, and you're ending up with something milky white, smooth-ish with brown spots, then there's no way to fairly judge the quality of the cheese.
Dialing back the toppings, as I talked about in the other thread, should also go a long way in helping your cheese bubble, especially if you're using watery veggies. Also, fat, as I said earlier, is a huge help. A larger quantity of pepperoni will be immensely helpful. Some of these supermarket brands say 'whole milk' on the label, but the actual fat content can be a bit low. On non pepperoni pies, a light spray of oil can help.
All of this, to an extent, goes away once you start dealing with Sysco, but you never can truly ignore the elements that go into crafting the pizza that bring out the most in the cheese.
You're grating the cheese by hand, right? No pre-grated or chunks/dicing, right?