In your electric pressure cooker’s cooking pot, combine the macaroni, 4 cups of water, and a pinch of salt.
Place a trivet in the pot and put the potatoes and carrots in a steaming basket on top of the trivet. Close and lock the lid and ensure the pressure valve is sealed, then select High Pressure and set the time for 5 minutes.
Once the cook time is complete, quick release the pressure, being careful not to get your fingers or face near the steam release.
Once all the pressure has released, remove the lid and carefully pull out the steaming basket with the potatoes and carrots. Transfer to a blender and add the milk, remaining 1 1/2 cups of water, salt, nutritional yeast, lemon juice, onion powder, garlic powder, and red pepper flakes (if using). Purée until smooth. Stir the cheese sauce into the macaroni. Taste and season with more salt or other seasonings, if needed.