You can use a thermal preload to shrink the bolt to attain the required pre load. You might need a multi step analysis so you would need the NL premuim version of the product. You could also use a shrink fit - just calculate the the required displacement - and make ht bolt that short with all the "interference on one side. I think the shrink fit you could use in a static analysis.
Pretty much exactly what you describe is how you might apply a bolt preload to a modeled bolt in your Simulation. You would just be applying equal and opposite forces to the faces of the bolt and hole shank that are interacting with on another. However, all interactions between the models would need to be No Penetration and in no way bonded. If you bonded the threads as you describe it would prevent the preload from applying correctly. I've linked a small write-up on the setup you are looking to do here for reference (GoEngineer - Simulation: Preload on Modeled Bolts)