For her those stories are so few, that it's not central to her in the way that it is for other mutants. So while yeah you could say they don't make sense, you can also find other reasons for them. Wanda's powers especially have changed so much over time that there is no definition for them. Chaos magic doesn't cover it, she didn't do reality warping on her own. Hex bolts and hex-pheres didn't cover it either. She had more going on than just mutant abilities. It could be easily written that she was misunderstood as a mutant because she had powers. So none of it really matters in the long run to the character. The mutant stories themselves have never really served her well. She has many more with being with the Avengers, or with Vision. So that is much more important to be told on her show. Even in the MCU overall.
Now, the discussion could be made that it's more of a loss to Pietro. He spent way more time on that side of the books.