I would agree that a tiny little surge protector won't do much, and that a battery is the main thing that that will prevent load-dump damage.
However, I'm not sure if turning the engine off on the car with the good battery is always an effective way of protecting against load dump.
If a car has a low battery, with not quite enough power to start the engine, but close, then its battery is plenty good enough to prevent load dump damaging anything. Also, in that situation, when only a little bit of help is needed, then jump starting from a car without running the engine is likely to work. But also, running the the engine on the good car won't do any harm. Even if the whole alternator output gets dumped into the battery for half a second, the voltage rise will be 1 volt or less.
The problem comes when a battery is really flat. The internal impedance of the battery will go right up, so it won't be much good at protecting from load dump. Jump starting from a car that isn't running in those conditions has two problems. Firstly, it often won't work. It's difficult to get jump leads and their connections to have a low enough resistance that you can actually crank the engine through them, and 12 V from one battery will not charge even a dead battery at all quickly. You need more like 14 V, which comes from the alternator of the good car. If the jump leads aren't making a really good connection, waiting a few minutes will allow some charge and the car will start after that.
Secondly, if you do get the car with the dead battery to start using jump leads from a good car with the engine off, what happens next? The alternator on the car with the dead battery will produce 14 V, but there is a risk that most of the alternator current is flowing back down the jump leads to the good car's battery. It's a good battery, low impedance, but it's just started an engine so the alternator on the previously dead car will charge it and a lot of current will flow in the jump leads.
Meanwhile, the really flat battery is still really flat. It will take some time before its impedance drops and it starts accepting charge. If the jump leads are disconnected, the current from the alternator will have nowhere to go, as the really flat battery isn't working and that can lead to load dump damage.
If you run the engine on the good car, the battery on the dead car will start charging before the engine starts, so it's going to make starting easier. Also as the battery charges, it's impedance drops, helping to protect against load dump. Then, when the engine starts, the alternators on both cars are producing 14 V, so there will be little voltage difference between the two cars, and little current flowing in the jump leads. If the battery on the previously dead car is still high impedance, the output current of the alternator will have reduced while the jump leads are connected.
With little current flowing in the jump leads, disconnecting them won't cause a load dump.