Place one 3½–4-lb. whole chicken, backbone removed, breast side up, on a cutting board; open up against surface as much as possible. Press firmly on breastbone to flatten breast (you may hear a crack). Pat dry and season all over with kosher salt. Place in a 1-gal. resealable plastic bag.
Whisk 1 cup plain whole-milk yogurt, 2 tsp. finely grated lime zest, 1 Tbsp. honey, 1½ tsp. ground cumin, ½ tsp. ground turmeric, 3 Tbsp. extra-virgin olive oil, 3 Tbsp. fresh lime juice, and 1½ tsp. Diamond Crystal or 1 tsp. Morton kosher salt in a small bowl, then scrape into bag with chicken. Seal bag and gently smoosh to coat chicken. Chill 2–12 hours.
Place a rack in middle of oven; preheat to 375°. Place 1 onion, very coarsely chopped, and 2 poblano chiles, halved, ribs and seeds removed, very coarsely chopped, in a medium bowl; drizzle with oil and season with salt. Toss to coat, then set aside.
Remove chicken from bag, letting any excess marinade drip off; place breast side up on one side of a foil-lined rimmed baking sheet. Roast until golden, 30 minutes. Rotate baking sheet front to back, then arrange reserved onion mixture on empty side of baking sheet. Roast until vegetables are softened and starting to brown, 14–16 minutes. Scatter ½ cup raw shelled pumpkin seeds on top of vegetables; roast until pumpkin seeds are golden brown and chicken is deep golden brown and an instant-read thermometer inserted into the thickest part of a thigh registers 160°, 15–20 minutes. Transfer chicken to a cutting board and let rest 15–20 minutes.
Transfer vegetables, pumpkin seeds, and drippings to a food processor. Add ½ cup cilantro leaves with tender stems, remaining 3 Tbsp. fresh lime juice, and remaining ½ tsp. Diamond Crystal or ¼ tsp. Morton kosher salt; process until combined but still a little chunky. Transfer salsa to a bowl. Carve chicken and serve with salsa and lime wedges.