We're going to need to ask for the following changes:
The ability for players to toggle whether their flight is on or off by default. If on by default, it will automatically turn on whenever the user moves from somewhere it's not allowed to somewhere it is allowed.
The ability of server admins to disable flight in PvP plots, to help ensure fairness so that we remain compliant with the EULA & MUG when selling non-competitive town flight.
It would be more-convenient to enable fly according to Elytra status than according to command.
This is probably going to have to be a request upstream, at https://github.com/TownyAdvanced/Towny.