There are two issues here.
Some companies forbid F/J simply as a matter of principle. Cost is a factor, but even when F/J is a relatively cheap or even negative delta, they won't permit it.
Others require a flexible ticket. There are people who do not have fixed travel and thus may well make 3-4 changes across a 7-10 day multi-city trip. They also have significant accounting issues in dealing with billing travel to a client and then dealing with travel credit. Thus, if they pay for flexible Y, the question is not whether one could fly in F/J for less, but whether one can fly in F/J on the same terms.
I am amazed at the number of companies who persist in small dollar pettiness. It is an eye-opener as someone who has been the beneficiary of flexible travel policies which focus on reasonableness rather than bean-counting.