Hi! I love tortilla type of pizzas. I learned from experience that it is best to saute the veggies first (usually onions, bell peppers and baby spinach) because like what happened in your situation, the veggies do not get done and the tortilla gets burned. Also, the veggies taste better that way, lol. Usually I bake them at 400-425 for 15-20 minutes, just until the cheese turns a bit brown. I use regular whole wheat tortillas and the flatout wraps with no rubbery textures or anything like that so it may be the low-carb tortilla you are using? Edges do get hard which is normal.
My personal favorite for is BBQ sauce as the base instead of tomato sauce, shredded/diced chicken, sauteed baby spinach and red onions. Yum!!