To be fair to the franchise, no previous movie, live-action series, cartoon (even including Scorpion's Revenge), book or other comic series has ever been canon, there's just the occasional element that gets absorbed into the games now and again. Even the games themselves clearly play it loose from game to game, so who knows what really is "MK canon", hell Special Forces takes place before Mythologies apparently yet Jax had his metal arms already. Sure it's a shame that something good like that technically doesn't count unless parts appear in game form, but it's not like there's ever been any spinoff media before that's truly been accepted as the real story.
It's one of those franchises a bit like, I dunno, Texas Chainsaw Massacre, or Hellraiser (but obviously way better than either as franchises, original movie entries notwithstanding), where you just have to kind of just roll with it from production to production.
