If using a whole squash, peel it, cut it in half lengthwise, remove the seeds, and cube the flesh into roughly 1-inch pieces.
In a medium bowl, combine the cubed butternut squash, cherry tomatoes and whole garlic cloves.
Toss the mixture with the oil, ½ tsp salt and 1/4 tsp pepper until everything is well coated.
Transfer the seasoned squash, tomatoes, and garlic to the air fryer basket in a single layer (work in batches if necessary to avoid overcrowding).
Air fry at 400 degrees for 16 to 18 minutes, shaking the basket halfway through, until the squash is tender and slightly crispy and the tomatoes are blistered.
If using a sheet pan, preheat the oven to 400 degrees.
Spread the seasoned mixture on a sheet pan and roast for 30 minutes until the squash is tender and the tomatoes are soft and blistered.
Transfer the hot, cooked squash, tomatoes, and garlic cloves to the bowl of a food processor. Discard any tomato or squash liquid that remains in the air fryer basket or sheet pan.
Add the fresh cilantro, lime juice, and 1 to 2 tablespoons of chipotle in adobo sauce. Start with one tablespoon and taste before adding more.
Pulse the mixture until you achieve a thick, chunky salsa consistency.
Transfer the salsa to a serving bowl.
Taste the finished salsa and season with additional salt and pepper as needed.
Serve warm or at room temperature with tortilla chips.