it is most likely that the bevel fixed it because it insulates the awkward topology on the top surface from the 90 degree corners. you could probably achieve the same result by insetting all the top faces.
I returned to the mesh without bevels, selected the top faces, and applied Mesh Display > Set to face. Now, all the normals are aligned with the faces: Thus, I managed to get rid of extra geometry (bevels), and the final result seems to be fine: I totally missed the tools for adjusting the normals. Also I tried to "break"…