I know for Indy, in our experience, they won't let the little one get past the height stick. With Indy you go off and do something else (Tarzan's Treehouse, perhaps?) or wait over near the "phone" after the first riders go into the queue (and get the switch pass). There are always a ton of people sitting along those rocks, waiting with their little ones.
I could see needing to wait in line if the line is crazy-long and well before the height stick area, but I think a better idea would be to have the non-riding kid and second-riding adult(s) wait at the phone and join the first rider when they get closer to the measuring area where the CM is.
You know, we go in the off season, and have never encountered really crazy lines. So the CM has always been easily walked up to, with no real wait ahead of time. And that might be coloring our experience.
DH verifies that for our trips where we used rider switch, DS only had to be pointed at, he (and I) didn't have to be in the line.