As I said in another post. Storymodes don't always come true. They never mention Shang Tsung in the story-mode yet Shang Tsung is in like 5 characters' endings. Out of arcade endings, only Liu Kang becomes ruler of the Netherrealm. Shouldn't Kitana's ending also allude to being a ruler of the Netherrealm?
On the contrary.
The story mode ending is what dictates what will happen in the next game, as has been the case since Deadly Alliance, for the last 5 canon MK games.
Arcade endings haven't predicted the story of the next games since MK3.
Arcade endings are the ones that are non-canon, ever since Deadly Alliance.
Quan Chi's MK9 ending had him betraying Shinnok and bringing Shao Kahn back from the dead as a phantom warrior, none of which happened in MKX.
AT BEST, some arcade endings can be considered to be semi-canon if certain parts of certain endings come true, but for the MOST part, individual character arcade endings should be taken with a grain of salt.
So, no, Kitana's ending could have her not being the ruler of the NetherRealm, but that doesn't mean that it
will happen for the next game, as you're implying.
Reptile, Ermac, Nightwolf, Stryker, Cyrax, Noob Saibot, Kabal, Jade, Sindel, Cyber Sub-Zero, Shang Tsung and Baraka's MK9 endings never happened.
The arcade endings in the MK games are just "what if" scenarios, much like the Liu Kang, Kung Lao and Kitana normal skins in MKX.
If NRS decides to make some of those "what if" scenarios canon, that's another story, but until they do or don't materialize in the next game, all that the arcade / ladder / tower ending really are are a bunch of "what ifs."
MK9 story mode had Shinnok and Quan Chi at the end of it, posing as the main threat against EarthRealm, and in MKX Shinnok was the BIG bad who poisoned the Jensei.
All of the dead warriors at the end of MK9's story mode ended up serving Quan Chi, and they continued to serve Quan Chi in MKX.
I'm 100% sure that Liu Kang and Kitana will be the NEW rulers of the NetherRealm, according to that post-credits MKX ending scene, just the same way that the ending scene after MK9 with Quan Chi and Shinnok lead into MKX with those 2 being the main villains.