Well, for one, despite the fact we actually have a literal Onett song now, Bein' Friends is still the default song for the stage. And Pollyanna remains the third most played song by default. Meaning that two of the three most common songs for the Onett stage are the town themes for Mother 1.
For two, and I'm not kidding about this, there is a fully modelled baseball field in front of the camera where it can never be seen in game. There isn't a baseball field anywhere in Earthbound, let alone Onett. Why is it there, and why is it still part of the stage?
For three, the layout is weird. Fourside is like an artist's interpretation of Fourside, taking place on a nameless building. Onett is built more like a straight rip from the game. So why are we on the Drug Store, with two buildings on either side that aren't near the Drug Store? And the Drug Store is also isn't far enough south relative to Ness' house.
Finally, thanks to Ani for this one, but why are the Runaway Five here? You don't see them until Twoson! Heck, they don't even play music or anything, so it's hard to even tell it's them! But if this was a Podunk stage, that could have been a Devil Car that was changed to the Runaway Five late in development.
There are other pieces to the theory, but these are the most important bits to the theory.