Prepare the pesto: In the bowl of a food processor, combine the pumpkin seeds, cilantro, lemon zest and juice. Pulse the machine a few times to chop up the ingredients. Turn the machine on and stream in the olive oil to make a smooth paste (use a few splashes of water if the oil wasn't enough to smooth out the mixture). Season the pesto with salt and pepper and set aside. Prepare the toppings: Place a medium saute pan over medium-high heat with 1 tablespoon of the olive oil. Add the bell pepper and onion to the pan and cook, stirring often, until the vegetables begin to soften, 3 to 4 minutes. Add the zucchini, garlic, red pepper flakes, and dried oregano to the pan and continue cooking until the zucchini is tender, 2 to 3 minutes more. Remove the pan from the heat and let the vegetables cool slightly.
Preheat a gas grill to medium heat. Lightly dust a work surface with flour and roll out the pizza dough to about 1/4-inch thickness. Lightly brush one side with a bit of the remaining oil and then lay the oiled side down over the grill. Brush the dry side with the remaining olive oil. Cook the crust until the bottom is lightly charred and the dough is starting to puff up, 3 to 4 minutes. Slide the pizza dough off from the grill and onto a baking sheet and flip the dough over so that the grilled side is facing up.
Spread the prepared pesto evenly over the grilled side of the dough. Scatter the cooked vegetables in an even layer over the pesto and then sprinkle the cheese over the vegetables. Slide the pizza back onto the grill, close the cover, and cook until the cheese is melted and bottom crust is deep golden brown and crispy, 4 to 6 minutes. Serve the pizza warm with additional red pepper flakes.
If you find that the bottom of the pizza is getting too dark before the cheese has melted, invert a baking sheet, slide the pizza onto it, and put that back over the heat. This will put some space between the crust and the flames and buy you a few more minutes of melting time.