Heyyo,
I also tried waypointing this level.. bots seem to not read "opens later" waypoints if the ladder's not there yet in the base cause the helipad's not built so they try n' climb up this non-existant ladder for a bit then decide to move on.
They know how to use the health and armor depots and get the ammo when hitting the buttons, but they seem to have a hard time with nading the crate to free the scientists.. I've seen them blow up bunkers twice, so that's at least something they can do.
I havn't seen them hit the beacon.. I should check into that..