Heat a grill or grill pan over medium-high. Spritz the pepper and squash with cooking spray. Grill until tender and grill marks form, 4 to 5 minutes per side. Let cool slightly, then dice. Transfer to a colander set over a bowl and let drain. Toss the drained vegetables with 1/8 tsp salt.
Preheat the oven to 400 degrees. Spritz the tortillas with cooking spray, brush with the lime juice and sprinkle with 1/4 tsp. salt. Cut each tortilla into 4 wedges and divide the tortilla wedges between 2 large baking sheets in a single layer. Bake until just crispy, 10 to 12 minutes. Transfer the chips to a rack and let cool.
Reduce the oven temperature to 350 degrees. Arrange the chips on an ovenproof platter. Top with the chili, grilled vegetables, cheese and scallions. Bake until the cheese melts, 6 to 8 minutes. Top with the pico de gallo and cilantro.