So apparently 3...e6 is not the main line at all then?
Your other points are fine, but this one looks a bit strange.
The mainline of an opening is not necessarily the move that is played the most often at any given point because some openings only develop or have signature moves later on.
For example, the "main line" of the Ruy Lopez starts out 1.e4 e5 2.Nf3, but 2...e5 is not the most common response to 1.e4.
Secondly, remember, part of my point is that part of the reason the Colle is disparaged is that it is too often used as a 10-minute opening repertoire. Just like other openings, you have to build a repertoire by sewing them together. So, there might be other moves more common than 3...e6, but in that case you are no longer playing "The Colle"
Thirdly, a move can show up infrequently and still show up more often than other moves, right? If there are 6 moves: A,B,C,D,E,F and A shows up 20% and each of the others show up 16%, then A is the most common] it just isn't very common.
In the case of the Queen's Pawn game, there are tons of pet defenses/deviations that take up the pie [just like a Black Sicilian player has to deal with a ton of deviations from people who do not want to meet the Open Najdorf.
I think it's worth remembering that this is only one line of the colle; a lot of whites pieces are positioned for an e3-e4 pawn push not played in this version. I agree it's not a threat to the best players but it is a simple system to learn. I have had good fun with it in the past otb, especially with a bishop sac on h7