Here's one more point:
Sometimes, I like to really crank up the settings in order to make an extreme-quality screenshot. I'll go in the external program, raise everything, pop into the game and slog as quick as I can through the massive framerate drops to avoid hurting the GPU, take the shot, pop out and fix it again.
Not only would only having the option to make the changes inside the client have the potential to hurt the hardware by meaning more time spent running with too-high settings (remember, high drawing quality can cause overheat damage; it's a future-proofing feature after all - although this is assuming 2.0 keeps using future-proof stuff like that), with the framerate crash and possibility of the game force-closing, it might actually be impossible to undo the quality upgrade again from inside the game.
Even setting aside serious problems, in this scenario not having a full-featured external config utility is bloody inconvenient.
But then I guess we're coming back to Raldo's point about being able to fix any option from outside the client being important, for the off-chance that a quirk of your system might lead to a normally innocuous change preventing your seeing or manipulating the in-client config menu.
Thanks for confirming that. Now.. How come you got into the alpha?! T-T