Simple lore change (you can expand on this):
The nether was a "test world" before the current one (the overworld) was created, testing different ideas. But when the overworld was made, the failed creations of humans and squids (Zombie Pigmen and Ghasts) were left to protect the world from anyone who tried to disturb what they came to know as their home.
OR, if you want, you could have ex nihilo make the nether have nothing but bedrock there and have:
There is a space between our world (the overworld) and some other world (if you have one) this place is completely empty, but it is possible to go there. No one knows why this empty void between our two world exists, and very few have actually gone there without any deformations. Many who enter become zombified, some gain the ability to fly, but on can fly because anyone who dies there become a ghost.
I am not good with lore, but that's what I'd do