At my employer, all travel bookings must be made via the same travel agency. If I don't, I apparently violate the contract between the travel agency and my employer (a university in Sweden).
A booking made directly via a train company is significantly cheaper than the same travel booked via the travel agency. Administrative overhead for the employer should be similar, because in one case they will get a bill to pay, in the other case a reimbursement form from the employee. Of course, there is an advantage for me as an employee to book via the travel agency; it's considerably less work. However, I personally like to figure out travel options and to be in full control, so I prefer to book by myself, even if doing so in my own time.
Why would an employer enforce all travel bookings to occur via the same travel agency, even if it's cheaper if employees book directly via the railway or flight company?