Perhaps the boss has seen employees booking itineraries to maximize UA or DL RPM credit at the company's expense and has seen enough of it.

The company is under no obligation to pay more to fly an employee the way he or she wants. Sometimes companies do ridiculous things -- I once had to talk my firm out of forcing me through a Southwest three-plane, two-transfer, eight-hour circus to save $25 -- and sometimes corporate travel providers are worse. But the RDM dimension of FF programs presents a moral hazard that employers have a right to counter by overseeing travelers' bookings.