How to seal straight-thread faucet shank / nipple to the faucet?
The scenario you've described is not ideal. The faucet was manufactured to a sub-optimal design. In this case, you must either select a different faucet, or improvise. Chicago Faucet has been using this same type of design on their wall and deck faucets for many years. They use an adhesive on their straight threads from the factory.

@DaveInCaz suggested you use a thread sealant. I would recommend an anerobic pipe thread sealant. Allow the nipple to cure into the faucet before attempting to connect your supply lines to the nipples. The torque you apply to tighten the supply line to each nipple could break the seal between the nipple and the faucet if you don't.

Your alternate choice is to select a different faucet.