Its very difficult to guarantee that waterstones are dead flat IMO even when you think you've done a good job on getting them so. You only have to read recent issues of F&C where David Charesworth goes to immense pains to flatten them and has developed his own strategy for using them to realize that they are more trouble than they are worth and much overrated, IMHO. I ruined a complete set of Japanese chisels using these stones and I am very careful what I do in the workshop. I now use DMT stones and a strop with jewellers rouge which easily gives a comparable edge and further you know that the stones are flat and will remain so.
Interesting opinion: I'd just observe that, while guaranteeing they're dead flat is indeed difficult, the same applies to all 'traditional' stones - eg water and oil - it's just that the issue is more prominent with waterstones.. One might also point out that DMT - or other - diamond matrix stones (or ceramic stones, for that matter) 'may' not be flat - and certainly, with time, my largest diamond plate has shown a change in the texture of the diamond abrasive in the central, most used, bit of the stone - I bet there'll be a measurable, albeit very shallow, dishing there.
So what am I saying? I think you can over-emphasis the degree of real-world flatness required. Yes, I do flatten my waterstones with each use. I use the 'crudest' of methods - rub 2 stones together under running water until they feel/look flat. This seems to allow me to get chisels and plane blades to the point where they'll cut any wood I wish to cut, so, frankly, I don't care how good the flatness is in absolute terms- it's adequate for my needs.
David's known for his perfectionism, and if I were, say, wanting to compare tools, I might take the time to get 'really flat'. It's not actually that difficult - rub under water as described, then 10 seconds on fine grade wet or dry on float glass...
Each to his own, but they are neither more trouble than they're worth, or over-rated in terms of the edge they give me... I'd not want someone to be put off without trying them....