Unless your dealer is certain you are only going to use that small allen wrench he is giving you very bad advice and, as AnkleWork recommended, get his advice in writing so you will have evidence when you make the inevitable warranty claim. Your 3" allen wrench is not going to over torque any of the bolts unless you are super strong but a torque wrench is a good idea anyway.

If the noise is the seatpost itself, get some carbon assembly paste and apply it to the seatpost and then tighten the clamp bolt firmly. If it's the saddle rails, you can torque them pretty tight since they are quite strong. Again, a torque wrench eliminates the guesswork.