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lynx-
Short answer is that you're bypassing the bikes regulator. And without knowing the car in question, it could put more voltage (engine running) into the bike than the bike can handle. It might not. But given that the bike will start just off the car battery, there is no need to run the car and risk anything.
So it may be fine, it may not. Why risk it when there is no need? If you know the voltage regulation of both circuit, then I'm sure you know enough to know what to do.
skinny
Don't run the car. Keep the car off and just use the battery.
The cars alternator could fry your electrics. The battery alone should be more than capable of starting your bike.