That's not a new twist, though.
That's literally happened with Armageddon (a bad guy winning), and MK9 specifically had the Armageddon ending modified so that it was Shao Kahn was the one who had conquered all and was about to bash Raiden's brains in with his hammer, right before he went back and altered the timeline.
You could technically say that the bad guys won in MK9, even though Raiden won the last fight (with the Elder gods help), because a lot of EarthRealm heroes died at Shao Kahn and Quan Chi's hands.
As a side note, I really hope that MK11 isn't just going to lazily be Armageddon 2.0.
I mean, the whole reason that the timeline was rebooted was to have UMK3 2.0 and for them to start with a fresh clean slate in that said new timeline, preventing Armageddon from happening again, no?
I don't want to see NRS go back to the whole Armageddon story, and I'm REALLY hoping that the timeline changes in MK9 and MKX reflect that.
Otherwise, if they go back to the whole Armageddon story then the reboot was all for nothing, story-wise.