You are confusing ‘stick up’ with the entire frontal area of the aircraft. They could make the the whole F-16 more flat but since they have to stick a guy in there that limits things so they don't bother. That design feature was built in at the beginning so it effects more than just the height of the canopy. Look at that picture again. From the top of the canopy to the bottom of the air intake it is 2 or three times taller than those unmanned drones. Since you can't get intake air past a human very easily a manned aircraft has, as a basic design constraint, the frontal area of a sitting human plus the size of the air duct to the engine. Those are fixed. Add to that the area of cross-section of a cockpit and you have more constraints on the design. An unmanned aircraft has other different constraints. In the case of the one showed, one of them is that satellite antenna.
Look, if you don't get why shaving even one foot off an aircraft's frontal area is good then this discussion is pointless and you need to go back to Aerodynamics 101.