There is actually ingame mechanics that will allow you to be picked by your ship while it is hovering above you. It seems to kick in when the game cannot find a suitable landing spot reasonably close to where you are located.
In my case this happened near Guardian ruins, located in some very hilly terrain. below there is a great spot to land two big ships like Anacondas. So when I was done and recalled my ship it would not always land, but instead hover above a ridge. Now this had me confused the first time this happened, as my Anaconda cannot have SRV hangar active at the same time as thrusters..... priority was set this way.
So the biggest issue I had was to navigate my SRV in a 45 degree slope to be under the cargo hatch, but once there, I could board my ship and be suprised that my ship was actually flying, and I just had to fly away.
I think this functionality could be tied to the use of NPC Pilot, and then allow us to have our ship follow us. etc. since we now actually have a Pilot onboard...