I used to use a Big Mouth Bubbler, which was not deep enough so about 3-4" of the rod stuck out above the top of the fermenter. I was worried mainly about loss of efficiency, so I wrapped the exposed rob above the fermenter in foam.
Specifically, I got some foam packing material and cut a hole in the middle, and cut it to length so it created a casing for the exposed rod. This was a hack, and after a few brews the foam got a little crusty and seemed like a sanitation problem.
So I got rid of that fermenter entirely and went with a Better Bottle that is deep enough for the whole rod.
Not sure if that helps, but that was my experience.