Is it permissible to add banking transaction fees (deductions) paid by the lender to the original loan amount upon repayment, so that the borrower bears them? And if it is usury, is it obligatory to request the return of these amounts?

What you did by returning the borrowed money without conditions or prior agreement is considered "حسن القضاء" (good repayment), which the Shari'ah encourages, and for which you will be rewarded, especially since you returned more than you borrowed. As for the bank fees upon deposit, if the lender requested you to deposit into his account, you are not obligated to bear them, but if you do bear them, it is considered "حسن القضاء." However, if he did not request the deposit into his account, and you were the one who chose this method, then bearing the bank fees is obligatory upon you, because the obligation is to return the full amount without any reduction.