(1) weight is not always worth it, notably when there are lots of climbs

(2) riding with others, need to be able to turn your head. Further, you can't get as super low when in a big group. It also doesn't help as much because the group dynamic is more important than crouching extra low and/or helmet drag

(3) out of the saddle sprints.

Because it doesn't work as much alone as in combination with specific aero body position. But you can't be in that position in a normal road stage because the aero handlebar extensions are forbidden in mass start stages.

Also there are less aero benefits to be had when you ride in the peloton behind other riders.