I think that placing trigger or variables on waypoint activation field really doesn't make a big difference if the unit doesn't enter the area of interesting.
The behaviour seem not to be the source of the problem as I've experienced the same problem with units both on "combat" or "aware" behaviour....
A solution could be setting a timed trigger that start when a unit of the second wave reach the grouping zone and then wait for a (reasonably) amount of minutes before moving on, so that a sufficient amount of units should be on place....
The only (but quite important) potential problem is the loss of firepower that the AI platoons could suffer, expecially if that squad is assigned to your platoon..... :-\