The X-Men exist in the same multiverse as the MCU. Fox’s versions of the characters have made a couple of cameos on the MCU proper. Sir Patrick Stewart as Professor X and Kelsey Grammer as Beast prove that the Fox Universe and the MCU share a multiverse.
However, every time there has been any time-travel adjacent adventure in the MCU, the Time Variance Authority, under the leadership of Kang, has erased the branching timeline, no matter where it is in the multiverse. However, before the timelines were ‘growing together’, where was the universe with the X-Men? And why did the TVA not interfere when Kitty Pryde routinely changed the course of time in the events of X-Men: Days of Future Past?
Kang is afraid of the X-Men for some reason
The reason that it is such a big deal that Wanda Maximoff, Doctor Strange and Monica Rambeau travelled to universes with X-Men was that Kang might have sealed those universes away. This is the reason that What If…? and Loki can only depict and work with universes that are at least in part identical to the main MCU timeline i.e. devoid of the X-Men.
Kang has also notoriously stayed away from dimensions with powerful entities (like the Dark Dimension with Dormamu) despite all the time-travelling shenanigans of Doctor Strange. Therefore, it might be the case that Kang, much like Rick from Rick and Morty, has grouped the universes under his control together, sealing away any threat to his power, which might come in the form of the X-Men or the Fantastic Four.
However, given that the X-Men have engaged in time travel and altered timelines without consequence, this leads us to believe that there is something about them that causes Kang to not interfere with their situation.
Who, or What, could Kang be afraid of?
Just like Dormamu, the X-Men universe has its fair share of cosmic entities that could put Kang on the run. To begin with, there is the Phoenix Force, both iterations of which have been proven to be quite powerful. Apart from this, other characters could pose a huge threat to Kang the Conqueror and his Variants. Apocalypse is a force unto himself, and along with his Horsemen, the mutant could be unstoppable.
Despite his multiversal reign, Kang has only claimed to have killed Avengers. He has never commented on the absence of the X-Men, or the lack of mutants in any of his appearances. While it could just be that the mutants are wholly unimportant in his eyes, it is also possible that the character has taken measures to keep them out of his way.
After all, Wanda Maximoff was billed as a mutant for the longest time, and Kamala Khan too has a cross-dimensional connection, being a mutant in the MCU. Kang has made some conscious effort to separate the Mutants from the rest of the multiverse, which could be the cause of his downfall in Avengers 5 or Avengers: Secret Wars.
