In a way I agree with you, but at the same time... we already have this problem now. My web browser — and I'm not going to name names here— wants to provide its own decorations. And put close/minimize buttons not where all my other window manager buttons are.
OTOH I don't use *that* many apps not built around my desktop environment/X11 toolkit. The ones I do use already look/feel different, so adding window decoration into the mix isn't going to peeve me much more than it already does.