Be aware of temperature gradients also. If ambient temp is 68° and you are using water that feels warm to your hand (say 100°) it can easily cause movement on an aluminum plate like an Atoma until the temperature stabilizes. The resultant lack of flatness won't really matter but it might cause you to lap off more stone than necessary because the plate is a bit warped. Then as it warms up it will change, so it will look like your pencil grid is being erased in a different spot. This happens on a lot smaller scale with the steel diamond plates and I don't know about the glass reinforced nylon ones, don't have any. It also makes my Shapton Pro stones move a bit. I always try to use room temperature water.
Stones being perfectly flat certainly isn't absolutely necessary but makes for much faster repeat honing on a razor when you come back to it, since you don't have to do any complex strokes to compensate for any areas that aren't making contact because the hone has a slightly different surface contour than the last time you used it. It becomes a bit more important if you do a progression through multiple stones - but even then they don't have to be necessarily flat - just if they're all the same contour it makes things easier and faster.
Personally I prefer flat stones but it isn't as though it's impossible to hone on a surface that isn't flat.
