The fees for the UPC tool are calculated by taking the product's weight and dimensions and using Amazon's FBA Fee Schedule (https://www.amazon.com/gp/help/customer/display.html/?nodeId=201119410) to get a fee value.
The Total Fees column includes all direct fees that Amazon will charge when a sale occurs. This includes both the FBA fee and Amazon's Referral Fee.
It does NOT include fees which are variable. It does not include inbound shipping charges, storage fees, or PPC costs.