I've never had to use any sort of RTV on a water pump/thermostat replacement. But also know that the torque spec is much lower than you might expect. 18 ft-lbs iirc, but don't take my word for it. One thing that can easily happen is that the t-stat can sort of fall out of the housing as you're moving it into place. In my experience it will leak like crazy if this happens. And on a related note, this soaked my gasket, but I had no issue re-using the otherwise new gasket. Somebody up above said install the gasket dry, but I believe they we referring to not using RTV.
And as a counterpoint to what others have stated, I've done several that weren't perfectly clean as described and have not had leaks. Which isn't to say they're wrong; I would still absolutely get it as clean as freaking possible. Good prep is the key on virtually everything in life. But if you can't get it perfect you may not need to have the mounting surface machined. I guess you only really know if you don't have it perfect and it leaks having controlled for all other variables.