A perfectly lapped stone is not perfectly flat, there is the grit and the microscopic space between them. If it were perfectly flat it would be called glass. What we are attempting to do in lapping is make the tops of the highest layer of grit on the same plane, not really make the stone perfectly flat.

Many naturals and synthetics benefit from lapping with a much coarser stone, refracting the grit and cleaning the area around the grit to keep the swarf from loading up. Think sandpaper sanding drywall compound.
The 325 plate seems a good general lapping/refreshing hone for most stones, but experimentation for your stone is the key. Try different lapping grits and see what works best. And forget about dead flat, even glass is not really dead flat… it doesn’t matter.