The first thing I would do is omit the sugar and dairy whey. Both of these, and especially the sugar, are known to pose problems in baking a pizza on a hot deck surface. What happens is that the sugars caramelize and cause the bottom of the crust to turn brown, and, in some cases, to turn black. This often happens before the rest of the pizza can finish baking. As you noted, if you wait for the top of the pizza to turn a nice brown, the bottom has had it and the cheeses can burn and develop brown spots. If for some reason you want to retain the sugar in the dough, you can bake your pizzas on screens directly on the deck. The screens will lift the pizzas above the surface of the deck so that the pizzas don't cook as fast on the bottom, allowing more time for the tops of the pizzas to bake. Some operators even use two screens under each pizza in severe cases. The negative of using screens in a deck oven is that another step is involved as you shuffle screens around. During slam time, this can slow you down and reduce throughput a bit. If you find that using screens results in a lighter bottom crust than you would like, you can always "deck" the pizzas by sliding them off of the screens directly onto the deck surface to get increased bottom crust burning. Obviously, it is better not to have to use screens.
Another possibility you might consider before eliminating the sugar and whey from your recipe is to try a lower oven temperature. You might reduce the oven temperature by 25 degrees to start and see if the problem persists. If so, reduce the oven temperature again by another 25 degrees. If you don't see improvement, then you can eliminate the sugar. You can try omitting the sugar first to see if that helps. If not, then omit the whey also. Of course, if you lower the oven temperature, the bake time may go up. This is something you will learn better as you play around with the different possibilities mentioned above. If you eventually conclude that the sugars are at fault but you still want to use some sugar, you can then try adding sugar back to your recipe but at reduced levels that won't result in overbrowning.
You didn't indicate what specific type of deck oven you are using. There are deck ovens that are intended to bake food items other than pizza. When operators try to bake pizzas in such ovens they sometimes discover that the tops of the pizzas don't bake properly, or as well as they would like, causing them to find improvisations so that they can offer pizza as well as the other food items the ovens can handle. It doesn't sound like you are using a deck oven intended primarily for items other than pizza, but I thought I would mention it just in case. Unless you have a fundamental oven problem, I think the problem is the sugars in the dough.
I hope you will let us know if you solve your problem. Good luck.