Basically because it makes maintenance hell. I work on a large legacy system where the "settings" description document is literally hundreds of pages (yeah, it's enterprise software). We have a setting for "should we show an application icon in the tray on the server when logged in via RDP".
Having a large amount of possible customizations for everything makes regression testing extremely hard as the number of possible permutations grow exponentially. Therefore, you have to spend a lot more time testing and checking and double-checking - resources that could have been spent improving the product instead.
Choice is not always bad, but it always comes at a cost. Sometimes that cost is substantial.