It’s the difference between a 3D (LNAV + VNAV) and 2D (LNAV + V/S, FPA, etc.) approach. With LNAV/VNAV you have lateral and vertical path guidance but with LNAV you are only getting a lateral path, hence separate minima.
There is also the steeper approach on the noise abatement trial procedure, which will have a different obstacle profile, as FlyingStone points out. The LNAV minima are the same as you are not using vertical guidance.