The MC from the Manga/LN series
A Wild Last Boss Appears is... kinda like this? less a myth more a historical figure since she is someone who was known to exist and basically ruled the world 200 years ago. but its commonely thought that today she is dead/forever sealed away.
Kumo Desu ga, Nani ka? MC eventually becomes known as a mythical monster known as the Nightmare of the Labyrinth and later
when she becomes an arachne and is sighted as such years later these sightings are viewed with skepticism and its thought the arachnee never existed.
hmm Oh just noticed the recommendations for
Making Magic: The Sweet Life of a Witch Who Knows an Infinite MP Loopholehad no idea it had another title, was excited because i found a new exciting witch story. but yeah thats a good series, even if it is sad at times.
Hmm, I can't think of any more off the top of my head but If you want a similar vibe go for MC's who are eldritch in nature, people don't think they really exist, are super powerful and usually just do what they want. some examples I found on this site that fit are
When a Creature of the Void fails to find friendship among her own kind, she instead sets her sights upon another, human-filled world. Unfortunately, humans turn out to be rather small and squishy things, resulting in a mostly accidental trail of death, destruction and madness as she embarks on...
www.scribblehub.com
and
To Enter Five Peaks Magical Academy you must have a familiar. Abigail hoped for a bird, maybe an owl like her best friend's, or a cuddly cat or loyal hound. She would have been happy with a particularly smart toad, even. Instead she got you.
www.scribblehub.com
there are other eldritch MCs i know and like on the site but they don't really fit the vibe i think you are looking for.
hmm, Um,. two of Funa's Series (LN and Manga) have the characters become so famous people pray to them, one of them actually has a religion founded worshiping her with out her knowledge but again its not really the same.
I'd love to hear if you have found more yourself since this post was first made though!