I believe the case deflector is different.
Correct. They fit, but the face is cut slightly different on the .40. That said, newer 9mm kits I have seen have the same deflector as the .40 but I have yet to see a .40 with the original 9mm style deflector.
My guess is that there was a need to alter the face for the .40 and instead of making two different deflectors, they just started using the .40 deflectors on the 9mm.
When I do .40 builds, I will machine the face of the LSC deflector to match that of the factory .40.