I think you need to:

1. make an invisible Helipad "Empty ==> Objects ==> H (invisible)", name it "getout"
2. Make sure you've assigned a "name" in your helicopter properties, such as simply "helicopter"
3. Set a waypoint for the helicopter directly on top of the H with "transport unload".

I think you're missing this text on the "On Activation" section of your LANDING waypoint (not your helipad, and no troop waypoints used): Add this to On Act: helicopter land "getout";

I think that's what makes the chopper actually touch down.

This is from Arma 2, I'm extremely sorry if the steps down carry over to Arma 3. I was just watching this video to try this tonight: http://www.youtube.com/watch?v=Kcqn2BvDqjs

I use a invisible H but it still hovers to high over ground. And even if its possible to fool the game using scripts and special wp's the game itself should solve this to make the editor userfriendly and also help in making the missions bugfree. You should not need to do anything else than placeing a transport unload and a getout wp and having them synced.

Closing due to lack of activity in over five months. If this issue is still reproducable for you, please create a new ticket for it or ask for this one to be re-opened.