Well since the topic has shifted from stone holders to flatteners, I'll cross post my response in another thread regarding my experience with the Atoma 140 for stone flattening:"I just got done making a BUNCH of stones for the EP - primarily Nubatamas but also Shapton and Choceras and 10k and 12k Superstones.
And flattening EVERY one of them. I'd estimate that's about 300 stones. Several DAYS of stone flattening straight. What do I use to flatten them? A 3x8" Atoma 140 plate. I used my plate on everything from the 15,000 Nubatama Bamboo stone to 1000 Grit Speckled Ume in two different hardnesses down to the ultra coarse 24 grit Nubatama Ume Aratae stone. And many inbetween.
And my 140 Atoma is still going strong.
I've used this same plate without replacing it for similar sized sessions too many times to remember. And again it is still going strong.
NOTHING comes close to this Atoma for holding up AND NOT sticking to the stones when flattening.
Most especially if you flatten both EP sized stones as well as full sized stones and are interested in getting a 'rock solid' foundation for your sharpening kit. I have gone through several DMT XXC plates. Over time the Atoma pays for itself in lower cost of ownership and ease of use.
For the EP - and WEPS, the Atoma plates are the best solution out there as Mad Rookie and most everyone else who has used them will testify. In terms of time saved reprofiling edges, if time is money, they solve the problem, especially for abrasion resistant steels. Available in 1x6" sized and also a 3/4" width for those working on recurved blades or who just want to save a few $$. Contact me directly for the narrower width."
So let's bring a subtopic to the front - flattening which method? - and separate flattening a grossly unflat stone from a slightly unflat stone and a fine stone from a coarse stone. If you have a grossly unflat stone - even a 15k Nubatama or a 30k Shapton stone - use a very coarse diamond plate - eg the Atoma 140. There's little sense in flattening with anything finer unless you need the exercise. In the other extreme, if you have a coarse stone - especially 500 grit or below, and it is already quite flat AGAIN use a very coarse Diamond plate. Why? Because a coarse stone flattened with a very coarse plate cuts more aggressively. One of the most extreme examples of this is the 220 GlassStone. Finely flatten it and it works poorly. Coarsely flatten it and it works very nicely. Conditioning the surface of the stone is texturizing the surface and it does alter the characteristics of the stone. In the extreme, using an Atoma 140 to flatten a 24 grit Nubatama stone puts too fine a surface texture on the stone and roughing it up with another 24 grit stone brings it back to life quite nicely. A 60 grit Nubatama stone benefits from 24 grit or 60 grit surface texturing.
IMO, using a finer plate to surface texture a stone in the sub 2k range is generally unnecessary, even moreso if it is a softer muddy stone like a 1200 Nubatama Bamboo, however something extremely hard like the double Xhard Ume 1k should get the scratches out as the stone wears so slowly. Here a 1200 or 600 diamond plate works nicely. A medium to soft natural aoto doesn't need texturizing, nor does a polisher like a Hakka as the mud fills in the scratch pattern quickly.
I'm not a big fan of using a coarser stones to flatten a finer one or vica versa as I prefer to avoid grit contamination issues. Here I find finer diamond plates a more universal solution. While this varies from stone to stone (relating to stone porosity), this cross contamination can range from almost none to quite severe. Also some stones can be flattened quite nicely on coarse stone flatteners depending on the stone flattener's formulation - like Choceras and Superstones, but don't do at all well on stones like Shaptons that are much harder and more abrasion resistant. Diamonds work on all stones.
An ideal surface texturing can be accomplished using a small piece of stone that is the same as the larger stone - a tomonagura. I sometimes texturize a couple of the same EP sized stones by rubbing them together or using an EP stone against a full sized stone for this. While true with synthetics, this is especially true with naturals.
'Nagura' is a heavily misused term. They are not all talc
There are the tomonagura, various specific natural naguras - Botan, Koma, Tsushima, etc and at the bottom of this list what I call cleaning stones , eg the 600 grit synthetic stones that come with Choceras that are used to clean' a stone surface (not recommended at all). While we often think of naguras as stones used to blend into the stone slurry for various reasons, original usage of true naguras was as specific stages in sword polishing as full sized stones, even predating the use of true naguras with straight razor honers for the purpose of generating coarser slurries on their finer stones (another idea I don't adhere to).
For the hardest of natural polishing stones, I highly recommend tomonaguras and feel it is worth the effort after initial flattening with a coarser diamond plate to texturize their surfaces with a 1200 grit diamond plate before going on to a tomanagura - which produces the finest best slurry.