My pals and I worked together to think of how World of Light works in smash bros. We came up with the headcanon that each universe (ex: the mario world, the splatoon world, etc) comes in two parts; a light and dark.
Light represents a better outcome, while Dark represents a worse and chaotic outcome.
For every universe, there is an equal and opposite counterpart.
Doc and Mario represent this, as Mario comes from the Light version of the Mushroom Kingdom, while Doc comes from the Dark version.
It's also good to note that not all canon characters come from the Light version of their world. We're still trying to figure it out, but one could argue that Olimar and the Inklings come from the dark versions of their universes sense they're from an apocalyptic Earth.
I hope this makes sense o_O I'll probably make more doodles to try and explain.