Sponsored locations behave weirdly with Pokéstop and Gym placement rules. They abide by some rules whilst bending or breaking others.
Typically, I’ve noticed that if there’s anything within a radius of where a sponsored location is added, it will usually result in the regular wayspot being hidden until the sponsored location is removed. I don’t think there’s anything the wayfarer team can particularly do about this, as sponsored locations aren’t a normal part of the wayfarer database, and the wayfarer team aren’t responsible for the proximity rules that the Pokémon Go team uses when it comes to Pokéstop and Gym placements, or how they interact with sponsored locations.