How do we reconcile the permissibility of repaying a loan with more than what was borrowed (if not stipulated by the lender) with the prohibition against the lender accepting a gift from the borrower (unless it is customary)?

A gift from a borrower is either conditional or unconditional. If it is a condition for the loan, then it is absolutely forbidden (haram (definition)). If it is not conditional: it is permissible upon or after repayment, but not before, unless there was a pre-existing custom of exchanging gifts between the two parties. The reason for prohibiting a gift before repayment is due to two matters: First: The gift might be due to the loan, which would then be usury (riba), because every loan that draws a benefit is usury. Second: The gift might influence the delay in demanding repayment of the debt, thus resembling riba al-nasī'ah (usury of delay). If the lender accepts it, he must return it or deduct it from the debt.