In that instance I've come to accept a bit of 'haziness' in the rules. While you are correct, that the computer itself would not take up that much room, other aspects of craft design are not taken into account at all (structure, sensor feed, redundancy, etc).
So if you assume the control section itself is relatively small (say .1 DT), the remaining space might be secondary computer nodes, storage, access to control area, power feeds, sensor feeds, control feeds, armor protection, rad protection, etc.
Everything (electronic) is already in place with human pilot. But, let's break it down. (A cockpit takes up 1.5 tons per crewman) This covers the electronics. The person would require ~1/2 ton for just the body. Another 1/2 ton for life support. (redundancy of systems is already assumed)
So, 1/2 ton + tonnage (if any) for advanced sensors. This would NOT be addition 1 1/2 tons for other crew positions as the electronics are extremely small.
1/2 ton for drones.