My thought was to have even heating on all sides - sure, it's close to 100w, but it will heat evenly and shouldn't be on very long. It's nowhere near hot enough to scorch or burn anything. If anything, I think it will run for less time than a shorter section, meaning the area of the carboy directly next to the element won't get as hot as if you were running a smaller piece that had to heat the entire volume.
Regarding the thermowell - I have two carboys but one controller. Assuming I'm fermenting at identical temperatures, and assuming both carboys have essentially the same volume in them, I would only need one thermowell. You need one thermowell / temperature probe per controller, and you can wire up that controller to heat as many carboys as you want as long as you want them all heated the same.