I know that you can damage the motorcycle battery by connecting it to a car or it's battery...for too long, the difference between boosting and charging. The regulator on a bike or car, for 12vdc systems regulates the output of the alternator/stator to a similar 13-14 vdc +/- to charge the battery. The current produced out of a bikes stator as compared to a cars alternator varies. When you connect battery to battery (car to bike) even though they are both 12v batteries, you have nothing in-between the connection to regulate the amount of charge that will be going to the motorcycle battery. Because a bikes charging system is different from a car's, and that the physical composition of the two batteries is very different, if left too long you will cause a buildup of heat in the motorcycle battery which could lead to battery explosion which may cause damage to the bike. This could happen wether the car runs or not. If the car is running the alternator senses the load and wants to charge all batteries at the same rate it charges the car battery. A rate that may be too high or fast for a motorcycle battery resulting in a situation where the battery could explode. If you are just boosting the bike you are not leaving the connection intact for very long. Same would happen if you used a battery charger where the regulator in the charger fails causing the battery to overcharge. It's not instantaneous, overcharging takes time, especially if the rockets battery is stone dead.
Where a car running could cause damage to the bike, not just the battery is if the peak voltage that comes from the cars alternator is higher than the peak rating of the motorcycle's charging system. This could happen if the cars regulator was not functioning properly. Normally if the regulator goes, you get no output from the alternator, not too much, but I suppose it could happen. Some of the larger trucks may have a higher rate of charge than some cars, all depends on how the system was designed. The only way to know is to take a multimeter reading across the battery of the vehicle while running, with a load, to see what it is charging at.
Based on theory there is no reason we can't use a 12vdc automotive system to boost a 12vdc bike, but we should not use it to charge a bikes battery. This is why in some cases when boosting we go positive to positive and neg battery post from car to chassis on the bike. This competes the circuit for the starter but does not provide a direct battery to battery connection. Personally I would use a car battery for a quick boost but I wouldn't necessarily run the car. Not that it's going to hurt anything but I don't carry a voltmeter with me to check to see if the system is compatible. If a car battery won't start the bike, there may be other issues.
I hope this all makes sense and doesn't confuse anyone.
Cheers