What you said, (total agreement): Now add pushrods to the equation, (no overhead cams), and one can see why these type engines float the valves at such low rpm's. What's cool about our bikes is not only the high redline but the torque available down low as well.
This is another benefit of the little valves, and the 'direct' action.... almost zero flex in the components, and since the only mass is the valve itself (plus the tappet, and shim) the springs don't have to be as strong.... so there's a lot less friction between the cam lobe and the device operating the valve. More engine power can go to the back wheel.....
As far as low end torque, there would be more if they had implemented something like the VFR uses, and operated the second pair of valves at a 'cut over' RPM.
Torque down low is mainly developed by how well the fuel is atomized. The injectors have helped with this a bunch, compared to big jets in simple carbs...... decades back, you couldn't get a motor that ran well at 6,7,8,000 RPM to run well at all, at idle. The valves were big, and stayed open for a long time.... good for high speed power because they could 'flow' a lot of air relative to smaller valves and less aggressive lift and timing. The trade off comes in how well the air flowing into the cylinders can rip apart the droplets of fuel.
The finer the droplets, the more surface area, and the more quickly the fuel burns. Rapid controlled combustion being the goal. Little valves on 'long stroke' motors with very little valve 'overlap' have strong intake vacuum... the air ripping into the cylinder breaks up the fuel very effectively.
Reduce the strength of that vacuum by increasing the volume of air (which 'slows' the air flow) and the droplets tend to be bigger..... harder to burn. That means less power for any given level of fuel added to the cylinders.
Variable valve timing has turned that on it's head. Now, you can have your cake and eat it too. Not only can you radically change the airflow, you can tailor the FI and the spark advance to match. The full blown SS bikes take that a step or two further, with the valve in the exhaust, and the flappers to change the volume of the air box.
There's so much adjust-ability there, the added weight and complexity of the vvt systems don't make a big enough difference to be included. The multi point laser drilled injectors make the fuel droplets way smaller than what can be accomplished with anything else, so the engine doesn't 'suffer' as much in the lower RPM portion of it's range.
I suspect the reason the FZ6 does as well as it does below 5K has to do with the 'simplified' intake system being tuned for mid range.
It's one of the most successful 'tuned for the street' racing motors I have experienced. Not much lost on top relative to the YZFR6 version, but it's more tractable.
The neutering they gave this rig going to the FZ6R is shameful. If I buy another FZ6..... it won't be the FZ6R.