I found this for those that are curious:
Apparently its fine - the issue is not the over charging or even the running/non running. Its the spark from the dead/low battery igniting a hydrogen explosion and royally screwing your day up by throwing acid all over you.
Right, they are both 12Vdc lead acid systems so there is nothing that could possibly damage one or the other. There is an established process by which one should connect and disconnect to minimize the possibility of injury.
I the case the car is running and the bike starts, you now have two charging systems of significantly different capacities possibly creating a conflict. There is a possibility the rectifier/regulator of the bike might be damaged if the jumper cables are not removed quickly upon starting. As the car battery has significant capacity to start a bike, and restart the car afterwards, it makes sense to me to take the extra precaution of leaving the car ignition off. Only as a precaution mind you.