When you say cooling system, do you mean as a source or a sink of the thermal energy?
High temperatures are crucial; from the temperatures mentioned they must be going for the exhaust system, where the most waste heat is available at high temperature. This suggests the exhaust system would be the best source.
If they need a sink, I think they’d try to use ambient air for simplicity. Ambient air’s advantage is that it’s cooler than the cooling system (duh!); its disadvantage is that it’s hard to get waste heat into ambient air compared to putting it into the liquid-based cooling system, which itself uses a fairly large liquid-to-air heat exchanger. In fact, if the existing engine cooling system took on the additional waste heat load of the thermoelectric generator, it would have to be made somewhat larger.
Due to thermodynamic considerations, the total (cooling+exhaust) heat rejection has to be at least twice the power output of the engine, in the steady state. Off the top of my head, I don’t have figures on how much of this waste heat the cooling system needs to dissipate; it must be in the tens of kilowatts under most conditions. Also, it would be nice to know exactly how this amount compares to the amount heat given off in the exhaust, which I think is the larger quantity.
Just some idle speculations here.
Source -- though I'll grant that the temperature is much lower than at the exhaust. But the cooling system offers a more efficient gatherer of heat from the engine, than just gathering heat from the exhaust.
Depends on the goal, obviously. If you're just trying to use the combustion heat more efficiently, that's a different story.
I think use of heat pipes works well in that environment, though.