Dave, you can have both a big salon and a nice aft berth.
Sure, my cockpit is higher than a aft cockpit, and I'm a lot drier because of it. Motion comfort is only a factor in a rolling side to side sea which is easily fixed by a slight change of course to either take the sea more on the nose, or put some more wind/heel on the boat to firm it up.
I'd have to guess, but I think my cockpit from floor to coaming is about 3.5 feet deep, the center well/floor is over the engine compartment. On the starboard side the passage way to the aft cabin is 'under' the coaming, full 6'3" tall. On the port side that area is used for the aft head.
I think it's nice to have two heads, one for us, and one for guests/wet storage.
Here's the view on mine from the salon looking out the hatch. Notice how low it is
Notice I don' t have an engine "compartment" - the engine is under the steps where the cabinet is. The top of the hatch is about shoulder height on me - making it easy to pass stuff up to the cockpit.