I can definitely understand what you're saying...and the two word comments can get you flagged, though typically this is when every comment you see in their comment tab that way.
I've been in the position myself before where I really wanted to leave something, but that's all I had, was a couple words. So I just didn't want to draw the line in this guide saying to not do it, but rather focus on the things that would get the positive response they were likely looking for.
But again..this is important for new people to know. Two word comments like great post at best get you nothing and can lead to being flagged. :)