I understand that historically pilot was sitting on top. And that radar on military planes should be pointed forward-downward and thus cannot be above the pilot(s). But in modern airliners there is so much space. And most important thing to look out for pilots is still the Earth. The Concorde even had a movable nose so the pilots could see better during takeoff, landing and taxiing.
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There were actually a number of early airplanes with a window in the floor of the cockpit. This was used both for navigation before radio navigation and satellite navigation was invented. And to see the runway during high angles of attack approaches when the engine blocked most of the view. But it was quite awkward for the pilots to be looking down and these windows were left unused.
Pilots do not actually look at the ground that much. The exception is maybe during the landing as they need to see the runway. But even then the runway is supposed to be in front, not bellow. And the cockpit have perfect visibility forward, where the airplane is actually going.
I am not quite sure where you are proposing the cockpit be installed. If you mount it under the aircraft there will be quite a bit of airplane between the pilots heads and the front. You could have the pilots lie on their stomach just like WWII bombers but that is an awkward position and limits the number of buttons they can reach. You might put the cockpit further forward so it is in the nose of the airplane. But the cockpit is quite big on modern airliners so you can not have it all the way forward in the pointy nose. You then have problems with visibility as a lot of the nose is in front of the pilots again. And there is no advantage to this unless you want to reduce the size of the instrument panel, but this is what pilots spend most of their time looking at.
As for the movable nose of the Concorde they did actually try flying with it up all the time and the pilots had no issues. They had enough visibility during takeoff and landing even with the nose up. So in the plans for an upgraded Concorde (which never materialised) the movable nose was deleted in favour of a fixed nose.
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