Yeah, you want the fans to run off the post-cooled (ie. bottom tank) water temp. The aim is to keep the water entering the engine at a consistent temperature. Running the fans off the pre-cooled water temp does not take into account the thermal efficiency of the radiator.
To take it a step further, the thermo switch should be mated to the thermostat being used. That way, the water flows (cools) when it reaches a certain minimum temp, and the cooling is boosted when it reaches a maximum temp.
If I remember correctly, I am using an 82 degree thermostat, and a 90/85 degree thermo switch (with a manual dash-mounted override switch). This is in my DR30 rally car, which uses the factory radiator. In 26 events, it has never had an overheating issue. Actually, I lie. It did once, and that was when the thermo switch failed. Hence the Tridon replacement. Fortunately I caught it in time and saved the engine.