If you have a router then it is very easy to flatten the top once you've got it glued up, so I'd just skip the dowels and clamp them boards up in pairs, then glue up the pairs, and then the pairs of pairs and so on until you have a top as big as you want. Let it dry, put it in place, and flatten with the router. (I like handplanes, but all the glue-lines make router easier.)
I'd also forgo the tempered hardboard or 1/4" masonite or all the other fake tops that are used to protect the bench. Tops get dinged, scratched, gouged etc. When it gets too ugly for you to look at, screw the rails on the sides and route off just enough to make it flat. That's one of the advantages of starting with a thick slab.
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