The three groups of cost
Lender charges are what the bank earns: origination or points, application, underwriting, credit and flood checks. Points are a percentage of the loan, so they scale with how much you borrow, and they are the line most often traded for a lower rate.
Third-party fees pay for work done on the property: the appraisal, the inspection, the title search, title insurance and the settlement or escrow agent. These are shoppable in most transactions, and the differences between providers are real money rather than rounding.
Prepaids are not fees at all. Property tax and insurance are collected at closing into an escrow account so that the first bills are covered, which means the amount is a timing difference: you pay it now instead of monthly, and it still counts as cash needed at closing.