I've seen both ways used. But it's not as common to have the thermostat probe inside the tub unless it's a dummy tub with no animal. I don't think there's a wrong way as long it's done appropriately. Personally, I tape the probe to the heat tape directly onto a belly heat rack. On a back heat rack, I tape on the shelf between the tub and heat tape.
If the thermostat is on the heat tape and is reading 100 and you're getting a steady 90 inside the tubs, then why does it matter? It's working isn't it. The thermostat is used to regulate the heat tape, but you shouldn't use the thermostat as a thermometer to measure the actual tub temps. That isn't the correct way to use it anyway. Plus a thermostat temperature reading may not be accurate anyway.. Always have a temp gun or some sort of thermometer device to measure enclosure temps.
My thermostats always read something else than my Acurite thermometers and temp gun.