Yeah, mutations are generally a BAD thing. It means cancer and death, and people exposed to a mutagen, like Mustard gas usually deliver still born babies or babies without skin or something to that effect.
But in a fantasy setting like DF, I can imagine villagers say "To the south is The Broken Hills, unspeakably horrible mutants roam freely there, you don't want to go there for any reason at all, seriously."
But like Toady is going to revamp the undead/evil biomes and regions he will allow the world gen to produce unique, random wildlife and a swath of tainted land nobody wants anything to do with, because its filled with nasty mutated horrors is perfectly within reason, I'd think. So long as it was relatively uncommon and all, and wasnt' linked to a soil type or whatever.
But once magic is implimented that sort of shit will be justified "Salvedangers the Balanced Squares of Malignancy cast fel magic upon the land in The Tainted Plains in 228, the cursed place is home to (insert mad-libbed mutant worldgen creature here) and nobody dares venture there"
As for mutant dwarves, most mutagens just straight up cause sterility, since people's berries tend to get effected the worst, but if you REALLY GOT TO HAVE MUTANT DWARVES, then I dunno. You embark on a hill in The Tainted Plains and all your pregnancies result in babies that come out with extra arms, tentacles, tails,or longer claws, medieval procedure would be to smash that fucking thing's head in with a rock, throw it in the refuse pile and try another pregnancy.
Just saying, even if pregnancies resulted in horrible monsters, the Dwarf Doctor would take one look at it and think "Hmm, thats not right, babies don't usually have that many eyes, or a proboscis, for that matter. Gonna have to get a specialist for this case, the Hammerer is better qualified to give the treatment this one needs."
But yeah, DF is to rely on "emergent" AI circumstances that come from randomly generated parameters or some shit like that. I'm sure something you'd like will result in future versions, good sir.