I don’t get it. Multiple frozen pizzas of different brands. They appear substantially identical in diameter, thickness and topping amount. Yet they have radically different temperature and time requirements for heating. I would understand if there seemed to be some correleation between higher temps and shorter cooking times but from my (admittedly limited memory and sample size) there doesn’t seem to be. So, yeah, mystified.
Different toppings make pizzas cook differently. Pepperoni has lots of fat, therefore, the pepperoni pizza will brown more slowly than plain cheese. Veggies have more water than meat, so they will cook through more slowly. Also, amount of cheese, amount of sauce, and size of dice of toppings and type of crust will cause variation in cooking. My frozen pizzas are all the same brand and cook at the same temperature for different amounts of time.
But as I said, they are all substantially identical in toppings, in fact all are plain cheese pizzas. So while it’s undoubtedly true that additional toppings will vary the heating times, that doesn’t apply here.
Each company experiments to determine empirically what heating process will consistently give the best results to customers. Even though the toppings may be “identical,” dough, cheese, and sauce can vary widely as to thickness, moisture content, fat content, and so on.
Of course, some of the differences may be somewhat arbitrary, and you should feel free to experiment. You might like a softer or crispier crust than what the manufacturer likes. Your pan might not be the same as what they used. You might not even use a pan. And have you calibrated your oven?
When taking frozen food directly from freezer to oven, I have found that lower cooking temperatures for longer times work best (for pizza I go no higher than 325[sup]o[/sup]F), otherwise you’ve got that burned-on-the-outside-but-frozen-in-the-middle kind of experience. I usually take the instructions on the box as a suggestion.
Just as long as you don’t suck your pizza through those little cocktail straws, you should be fine. 
There’s probably also differences in the compositions of the cheeses. One cheese might be fattier, one might be waterier, and one might have a greater proportion of milk solids, but they might nonetheless look and taste roughly the same. And those three cheeses would probably heat at different rates. There might also be differences in proportions, with one brand having more sauce than another, or more cheese. And the crusts might have different densitities, or have differently-sized bubbles in them, which could also make a difference. For that matter, the dough might not even be cooked completely before freezing, and might be cooked different amounts for different brands.
And it may even be that the test cooks for the different companies have different tastes on just how cooked they like their pizzas.
Put me in the “it doesn’t really matter” camp. I rarely bother to look at the temp or time when cooking- 350 until it looks like food works for just about everything. Chances are the frozen pizza makers just make their instructions up based on a few test times. They arn’t really going to bother to coordinate with other pizza manufacturers.
I’ve noticed that effect too, with pizza right out of the freezer. I sometimes cook it in the oven, then finish it in the microwave when the pizza isn’t thawed first. I’ll have to try your idea!
For something as simple as frozen pizza, a rather wide range of temperatures will work well. Personally, I like thawing my pizzas out just a little bit and cooking in a very fast oven (450-500 degrees). This produces a very nice level of doneness and crispiness.
However, there’s simply no one right temperature for pizza. One manufacture may find a softer, more pliable crust is appropriate to their product and suggest a lower temp; another may be going for the cracker crust effect and indicate a higher temp.
What CookingWithGas and Chronos said. I can make lots of different cheeses with lots of different compositions that all look and taste “identical” to the layperson. Same with sauces…same with doughs…