That’s my preference: that Mutants traditionally show up more in times of extreme stress, stimulus, and luck, and thus were generally rather rare and passed as legendary heroes and demigods... and were even rarer in the past centuries of human history in the MCU due to the progress of technology making decreasing their chances of developing in some areas decreased and the chances of being hunted down increased as well...
...And then the Snap simply increased the chances of survivor to develop mutations at a much higher percentage than previously... but still as a clear minority small enough that demonizing them gets even easier for people looking to find someone to blame for their problems. And I’d maybe have their be three divergent theories about mutants - one side sees them as a natural “defense mechanism” of humanity, another as evolution (cue Sinister as the main proponent of this theory), and of course a third thinking that their unnatural creations springing from the Snap and Thanos so that a lot of misplaced anger can come from that.
Here’s a thought for Wanda and Pietro (both of him) for a second: what if the reason they survived the experimentation was because they were mutants, and din’ know it, so the mind stone supplemented and made them aware of their powers instead of just conferring it upon them?
Honestly... I don’t think the MCU would lose much by introducing mutants as early as possible, and simply making it background issue while things grow tense across their creations.