As has been noted, you don't really need a back story for the various magical creatures. I'd note even if you decide on a detailed back story you don't really need to come up with game mechanics unless it's likely the PCs want to get in on the action. You just need a back story.
There's a number of fictional precedents which deal with the origin of magical species. There's the otherwise forgettable old rpg called
Fifth Cycle that explained dungeons, magical races, monsters and artifacts as the consequence of a previous age of lost high magic. Kind of a Gamma World back story for old school D&D. There's also James Kahn's World Enough and Time which is an After the End setting where genetic engineering created elves, centaurs, monster etc just before the end. Original D&D has something of a post-apocalyptic vibe.
That in turn could lead to lost secrets of creating magical creatures as a treasure or alternately something that needs banishing. In general I think it would be more useful to look at the implications for the world than working out game mechanics.