Is it permissible, Islamically, for an employee to put in an expense report an exchange rate for a currency that differs from the exchange rate at which the actual payment was made, leading to a financial gain for the employee?

It is not permissible to take a financial increase (more than what you were authorized to take) without the company's permission. Otherwise, it would be considered deception and betrayal, because any increase earned by the agent reverts to their principal.