If I understand the post correctly, your trying to keep the wood from having a glossy look to it. Water based poly will have the least ambering effect to it, but even a flat poly will have a slight sheen to it. If its too much gloss, go to your drug store and get an unscented and unmedicated talc powder and add a couple of level tablespoons for each gallon. Test this first with a small amount of poly and a small scrap of wood to see if the effect is what your after, and that the talc is compatable with water based poly.
I've used this trick with oil poly, I've never tried it with water borne material.