As Randy's cite indicates, your actual question is "are these items Finance Charges?" Each item must be judged separately and all that are FCs must be reflected in the APR. The only remaining question would be "how?"
When a borrower's contractual obligation to pay a FC is satisfied at or before consummation, then that makes the fee a Prepaid Finance Charge and it hits the APR up front. In other cases, the fee would be a garden-variety FC and would be included in the APR as part of the payment schedule.
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...gone fishing.