Turn on the saute function and heat olive oil in the Instant Pot base. Add the onion and cook until softened. Then add garlic, thyme, paprika, and red pepper flakes; cook until fragrant, about 30 seconds to 1 minute. Cancel the saute function.
Add dry macaroni, cubed butternut squash, and broth. Stir to submerge the pasta in the liquid. Attach the lid and set the valve to sealing.
Cook on high pressure for 3 minutes. Once cooking has completed, quickly release the pressure.
Switch to the saute function, and stir in butter, milk, and shredded cheese. Continue to stir until the cheese is melted and smooth. Stirring will also help break up any remaining cubes of butternut squash.
Notes
Squash: Other varieties of squash or even pumpkin can be substituted for the butternut squash if desired.