xanth might be along shortly to answer for himself, but fwiw, I tested and verified that if, in the mission editor, you set a chopper to any flavor of "mount if ..." it has no apparent effect.
I right-clicked on an empty Blackhawk in the mission editor and set it to "mount if this unit is not carrying troops." I routed it with march orders directly over a squad at treetop height, and it happily flew right past them -- whether they were its own native troops or a random unit.
But when I
instead set the ROUTE or a PRECEDING CHECKPOINT to "Mount" or "mount if ..." the chopper dutifully stopped and landed about 100 meters short of the squad and picked them up.
Setting the route/checkpoint logic can be done in the editor, in planning or on the fly.
So, the answer to xanth's question is yes, a chopper will pick up "random" friendly troops: He needs to set the logic for the route, not the chopper. Beware though, the chopper will continue to stop and load up any friendly infantry it encounters until it runs out of seats or you intervene to give it a new route.
Whether the inability to set the logic for the unit itself is intended behavior or a bug, I don't know.
Next did you land the helo at the said waypoint?
Unnecessary. The ai pilot will land to pick up troops automatically from any flight height if he has route-based "mount .." orders.