Mortal Kombat 1 is both a reboot and a sequel, following on from MK11's ending in which Liu Kang became the Fire God and reshaped reality. However, in his new peaceful Utopia, Mileena is still a Tarkatan hybrid, which has fans wondering why Liu Kang didn't just make her Kitana's twin sister once and for all.
Mileena's history is tragic. She was born in Shang Tsung's flesh pits under the order of Shao Kahn, fusing Kitana's DNA with Tarkatan blood to create the ultimate fighter. This twisted beginning led Mileena along a bloodthirsty path to kill Kitana so that she could take her place. Eventually, in the new (now old) timeline of Mortal Kombat 9, she became the ruler of Outworld and forged her own story, but she was overthrown by Kotal Kahn. In MKX, she clawed for her reign back, only to die at the hands of D'Vorah. But with a new universe comes a new Mileena and a new chance for peace.
It looks like in Fire God Liu Kang's universe, Mileena and Kitana are not rivals or enemies, much like with Scorpion and Sub-Zero. This may be Liu Kang's attempt to right the wrongs of the previous two timelines, but that still begs the question of why Mileena isn't just Kitana's twin. One theory suggests that Liu Kang can't reshape reality in minute detail, he can only paint broad strokes. This means Mileena would stay the same, perhaps even having a similar origin story, but would not end up lusting after Kitana's death.
Supporting this theory is that in MK11, we find that Kronika couldn't control the universe to that degree. As such, it's likely that Liu Kang is simply reworking the tools at his disposal to try and bring forth peace, but when your tools are drenched in the iconic blood, bones, and guts of Mortal Kombat fatalities, violence and chaos are inevitable.
Another theory that ties into this is that across the Mortal Kombat universe, there are constants. Think of Doctor Who's fixed points in time that nobody, not even Time Lords, can change. In this case, events Fire God Liu Kang cannot rewrite. Mileena being born half-Tarkatan at the hands of Shao Kahn may be one such event, and Liu Kang has no sway over the matter.
Less grand than these two theories is PepperBun28's, which posits that Liu Kang put the pieces back together in a new order and then sat back to see how things would unfold. He wanted to see if Mileena and Kitana could get along without changing too much, observing their behaviour. It's certainly possible, if a little creepy.