At the time Disney / Marvel had not yet purchased Fox's assets, so they rewrote the Maximoff twins into a product of experimentation. Marvel also retconned some other mutants in the comics in similar ways as well, since Fox had the rights to portray any mutant on-screen.
There's been drops that mutants exist in the Miss Marvel and She-Hulk shows, though. So we know they're in the MCU now.
ManaByte
could definitely fill in the details if you wanna know. I've seen him explain it in the past. I just know some surface-level stuff and I probably have the minutiae jumbled in my head.