Preheat oven to 425 degrees. Line two sheet pans with parchment paper.
Combine butter, miso, honey, and rice vinegar in a large bowl and mix with a rubber spatula until it is well combined.
Add chicken to the bowl and massage the miso-butter mixture all over it. Place the chicken in a single layer on one of the prepared sheet pans, sprinkle with a pinch of salt and set aside while you prep the squash.
Peel the butternut squash with a peeler. Cut the squash lengthwise and scoop out seeds. Turn the squash cut side down and slice into ¼ inch thick half moons.
Peel the kohlrabi, slice in half lengthwise, then slice into ¼ inch thick half moons.
Toss squash and kohlrabi, with 2 tbsp oil and salt and put on the other prepared baking sheet. Place both sheet pans in the oven and roast until the chicken is fully cooked, 20-25 minutes (if you use bone-in thighs they will take about 35-40 minutes).
Remove the chicken from the oven.
Continue to cook the butternut squash and kohlrabi until tender and golden. Then sprinkle the pumpkin seeds over the top of the cooked squash and kohlrabi, reduce the oven temperature to 350 degrees, and roast for 3-5 minutes until the pumpkin seeds are slightly golden.
Meanwhile, whisk orange juice, lime juice, vinegar, miso, and crushed red pepper in a small bowl until miso dissolves. Stir in cilantro; season with salt if needed.
Serve the squash and chicken drizzled with citrus mojo.