Supposedly that possible, but the real question is, if this still will be the case in 10.12? This concern was posted by someone somewhere few versions back, when they introduced code signing explicite allowance for apps not signed properly. This is next step. And as long, as I agree - security is important, judging on their past decisions, they may try to close their ecosystem (but hey, it's "their" hardware and software, their game and their rules - one can always decide not to buy Apple anymoe).
It would be very out of character of Apple if it weren't configurable. Yes, iOS is secure, but OS X has always been more open in this regard and there's really no reason to believe that they won't continue this trend.
After all, when they introduced App signing they could have made it so the mac would only run signed apps.