Yeah, I'd think when you bake on any kind of pan, it takes at least a few minutes for the pan to reach the same temperature as the stone. At the same time, the pan is taking heat from the stone. Especially cutter pans, which are pretty thick and very dense.
So basically, the way I see it, when you bake on a cutter pan, the first few minutes of baking is essentially a form of proofing the dough in the pan. Which means such a pizza will be more airy and a little thicker than the same pizza baked directly on stone.
I've gotten to the point where I always prefer to bake without a pan if possible. Some styles just don't work that way, though, because certain pizzas have to take the shape of the pan. Like deep dish, stuffed, and PH thin. You can't make any of those styles without a pan.