One point of confusion is the use of a nagura on
a very hard hone stone.

Think of it as loose abrasive on steel or glass
substrate. The a natural stone will have a bit
of tooth that abrades the rubbing stone that establishes
the effective grit. As the grit is pulverized the substrate
becomes a hard polishing base...

Other natural stones are rubbed to release abrasive bits
in the hone material itself like a coticle.

Another turn of the rock is the Arkansas hones. All
are the same mineralogy with an abrasive hardness
that is the same as quartz. The abrasive hardness
never changes but the hardness as measured by density
does. The denser/ harder Arkansas is considered the
finer hone even when the grain size is almost constant.