Techniques are provided for programming and reading memory cells in a 3D stacked non-volatile memory device by compensating for variations in a memory hole diameter. The memory hole diameter is smaller at the bottom of the stack, resulting in more severe read disturb. To compensate, programming of memory cells at the lower word line layers is modified. In one approach, threshold voltage (Vth) distributions of one or more data states are narrowed during programming so that a lower read pass voltage can be used in a subsequent sensing operation. A sufficient spacing is maintained between the read pass voltage and the upper tail of the highest data state. The Vth distributions can be downshifted as well. In another approach, the read pass voltage is not lowered, but the lowest programmed state is upshifted to provide spacing from the upper tail of the erased state.