Is it permissible to take a small commission exceeding the commission charged for services like "Fawry" or "Naqdan," in the event of using a personal visa card to complete a government financial transaction that requires payment by visa card, and is it permissible to take an additional commission to cover withdrawal fees with a small increase on top of them?

Your enabling another person to use your bank card is considered a loan, and it is not permissible for the lender to derive benefit from their loan. Therefore, any increase on the amount is impermissible. The permissible alternative is for you to receive the amount first, and then its owner authorizes you to pay on his behalf. This would then be an agency for a fee.