I blame this on Blender/SubstancePainter or the importer. Flipping something reverses the winding order of the faces, thus reversing the normals. SketchUp is wisely designed, knows when an object is flipped (has a determinant less than 0) and compensates for the reversed normals. Somewhere this isn’t done when importing to Blender.
Does Blender recognize the two objects as identical, i.e. sharing some kind of definition, or are they just two separately defined meshes?