As the substrate height varies, the system must correct both focus and field size. The depth of focus is actually quite large– several microns. Correcting the field size is more critical, since this determines field stitching accuracy. You can see now why smaller field block sizes lead to smaller stitching errors.
On the EBPG you should keep the block size less than 700 um so that field stitching errors will be less than 50 nm. The maximum block size is equal to the maximum field, 1 mm. But it would be a mistake to use such a large deflection.