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Caulking or 100% scilicone does not last the life of the roof and should not be used. what you are refering too is a salesman way of saying that we go out of our way to do a great job for you!
Then again this is just my opion
Maybe what your contractor was refering to was they were installed inproperly.
most of the leaks that I encounter are form chimney flashings where the flasing and the counter flashing were fastned together and the could not move when the chinmey shifted.
If your going thru the bidding process, be very careful of any roofing contractor that wants money up front. There is no reason why one would ever need money before the job is started!