As Soukyuu says, some options would probably require the game be restarted to work. I think Anisotropic filtering is a particular offender in this regard, for instance. Depending on the start-up times for the 2.0 client (especially if they keep the login external), being able to edit settings that would require the game be restarted from outside the client could well be more convenient (it certainly is at the moment).
Hell, it's pretty much the fashion these days to provide an external config program if your game has any options that would require a restart, and give it the ability to edit all settings, restart required or no.
Frankly, that is what they ought do. Keep settings would require a client reboot in the external config program (and possibly put them inside the client too, tad redundant though that may be), and then make it possible to edit every configuration option that wouldn't require a client restart from the external program as well.
Removing options from the external config program (or indeed, removing the program itself) is counter-productive in my opinion. They should just be adding things that can be edited in-game to the in-game Configuration menu as well.
Oh and it might also be nice to be able to access the in-game Configuration menu from the Welcome Screen too, so as to not have to go through loading up a character to tinker with the settings.