Here's what my limited knowledge tells me.
Automatics are predictable, they will change gear at a certain time, every time. Manuals are controlled by you, you can either choose to drive your sports car in an eco friendly way, keeping your revs down or drive it like a madman over revving your engine and burning tons of fuel away.
The government, i can only imagine, assumes that everyone owning a manual transmission sports car falls into the latter category...
Although everything i've ever read about Manual Vs Automatics says the opposite, that manuals are infact more fuel efficient. So i can only assume the above, that the government thinks everyone drives around at 30mph in first gear all the time, wheelspinning at traffic lights and tokyo drifting around....tokyo...