If you are using the new build, there should be an option for assisted landing, which automatically deploys the gear when near an active runway. No need to press Q&E. The option should be turned on by default.
Is this a problem unique to the pirate side? Can you land in the other ending?
Just to confirm. To land in the pirate ending, you have to select the pirate ships runway as a target to activate it. Then you can land on the deck. If this is not possible, it may be a bug. And a pretty big one too! Please let me know what you can, so I can confirm.
There is also an upgrade part which automatically skips the landing sequence if you fly near an active runway.
Viewing post in How to land the craft in mission three (pirate side)
Looks like selecting the landing target with F helped with the issue.
The game controls manual did clear things up, but I feel like it's the sort of thing that's easy to miss if you play the mission without reading the manual first. Perhaps a later version of the mission could incorporate a small in-game popup to select the runway target with F?