The OEMs see a 5% improvement because they hardly use the cylinder deactivation. They don't use it at idle, or under moderate load. Mostly just during cruising. An ecomodder would use it much more often.
They deactivate the valves so that they can run the 4 cylinders with the best balance, so that the customer only sees a little vibration at certain rpms. They have to keep the air from coming in or out of the chamber so it doesn't mess with sensors.
On my Mustang, there are separate O2 sensors for each bank, so I could turn off fuel injectors from one bank, fake the signal from the O2 sensors, and the ECU would stay happy. The air from each bank joins after the sensors, so O2 from the one bank shouldn't get to the other bank. Honestly, the only problem I see is how bad the vibration is.
For your project, what you are looking at I think is basically individual throttle bodies, maybe sealed up better. The 3 valve 4.6l has flaps inline (Charge Motion Control Valves - Tumble generators) that could be turned into full fledged valves/throttles.
