The rates from FedEx when calculating inside NetSuite may be lower than the website due to the reason below:
With FedEx.com, if an account number is not used with the rate finder, you may receive a "counter" rate. The base rate for counter rates will be higher than a list rate obtained with an account number. These counter rates would also apply to someone who drops off a package at an authorized service center but does not have an account number. The incentive here is to have and use a FedEx account number.