Why would it? Just register the plane as having a certain MTOW and a range of flex weights. Those flex weights are used for airway/airport charges only.
We use a similar system for quite a few years now and crews can decide each sector which of the 10 different flex weights they use, of course it is always the lowest possible one. In the near future there will be no crew decision about that anymore, centralized load control will use the lowest possible MTOW for each flight, the crew doesn't need to do a thing. Oh, and i'm not flying for ryan air of course.