Flat is good, tiny scratches do not really matter when honing.

I use a translucent small Arkansas( ¼x¾x3")pocket knife stone to clean my stones after using and lapping.I will not shed any grit as it is harder and finer than any stone I own other than itself. Specially good for Shapton glass which are soft and wear quickly!

After the steel rub on your Atoma, try using a hard Arkansas hone to mellow it out. They will take a lot of rubbing on diamond!!

YMMV
~Richard