Some random thoughts on lapping ceramics:
Use something coarse and tough like a XXC DMT to get them flat. Then use finer abrasives like wet-dry sandpaper to achieve the desired finish.
There is a natural tendency for the medium rods to get smoother with usage. For instance, a medium rod that is worn out from long-term heavy usage is going to be smoother (i.e slower cutting). So if you start lapping these ceramics, it might be easier to lose cutting power than to recreate it, especially for the medium ceramic. (Spyderco does not recommend lapping.)
I'm not sure the flat sides of the ceramic rods are meant to be dead flat. Wouldn't a very slight convexity be more useful. For sure, any hollowing would make them useless. Also, it would be difficult during normal use to hit the sweet spot on a totally flat surface. A little arch would help to keep you somewhere on the surface, whereas with total flatness you would always be on one edge or the other.
My lapped UF bench stone is so smooth I'm not sure it even cuts anymore. I used it to touchup a 50-year old razor last night. I rubbed the UF on a 12K waterstone to pick up some 12K slurry. After a dozen laps on the UF with the razor and the slurry was turning grey from swarf. Then I washed off the slurry and did more laps on the UF without slurry. Then a few dozen laps on 1 micron diamond lapping film on glass. Then some stropping laps on nexcare tape on glass dusted with 0.5-micron chrome oxide. This morning I stropped it on a leather hanging strop and shaved. Ahhh, feel the glide!