While a load on the soil at point A will certainly affect the soil deflection at point B, most engineers feel that Winkler springs are reasonable engineering approximation for most structures (with modifications to ensure no soil tension).
A true analysis would need to consider the soil as a 3D continuum; that type of analysis is only appropriate in a small subset of specialty structures.
As a compromise between these two extremes, some engineers will use a varying subgrade modulus that is stiffer at the exterior of the foundation and softer at the interior. Geotech references (such as Bowles) can give guidance on how to calculate reasonable values. You will need approximate foundation dimensions and bearing pressures as input for those calculations.
