I ferment in glass, and put the sensor in a thermowell that passes through the stopper. So I'm measuring the beer temp directly. This also makes it possible to use a 1 degree differential.So, having just 1 controller means just 1 probe. This is not to say, though, that this is the only way to roll. Plenty of brewers just tape their sensors to the side of the fermentor and cover it with some sort of insulation, and get good results that way. If you take that approach then having two separate controllers would work just fine, I'm sure.
That's the advantage of the ETC-211000. One probe. Alternatively this guy www.brewershardware.com can make a dual sensor probe so you can put two sensors in one thermowell and use two controllers.