As @mikebind suspected, the vtkWindowedSincPolyDataFilter normalizes coordinates (rescales the input to a unit cube if NormalizeCoordinates is enabled; which it is), therefore the smoothing result depends on the bounding box size. In general, the difference should be negligible, but it seems that it is possible to see a perceivable shift in real-world applications where the ROI size is very different along the 3 axes.
Disabling coordinates normalization fixes the issue, but I’ll need to check with Will Schroeder (developer of this algorithm) what other issues it may cause if we skip normalization.