The old RFTG program, which can easily be found on the internet, has toggles in it for turning on and off Takeovers, Goals, and 2 player advanced mode. And apparently the publisher, Rio Grande Games, gave permission for the program to be freely distributed. It just depends on what sort of agreement BGA currently has with the publisher. The ability to turn Takeovers on and off is already on BGA, but the other options would be nice for players who desire them.
But yes, having a toggle for turning on and off Prestige mode may not be a good idea, as I agree that some some cards become essentially worthless, such as Interstellar Casus Belli.