I'm not sure it necessarily leads to more fragmentation if it allows the creation of a Wales & Borders IBU.I don't see further fragmentation of the railway system as at all desirable.
I think that the more interfaces are created the more hamstrung any attempt to deal with the railway's problems will become.
Under the status quo the people of Wales have a say over the operation of Network Rail in any case, and the anomalies of today only get worse if the Welsh government obtains control (or de-facto control) of railways in England.