Actually, I have a five-speed manual transmission. Also, I drive around with the electric motor disabled all the time, because I save gas by avoiding the constant motor->battery-> motor energy conversion losses.
The battery pack has a current sensor that outputs a voltage proportionate to current. The efficiency of the inverter and motor, once warmed up, vary with RPM and load in a knowable manner. So it would be possible to account for the torque from the electric motor, but you'd probably need a lot of dyno time to come up with the efficiency map of the electric motor for each model of hybrid you want to support. I've come across maps for the Prius, first-gen Insight, and Honda Accord V6 hybrid.
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