It's a bit tricky to explain.
That's the rule: the moon lander will spawn at the same coord of the point when you exited the previous dimension.
For example: you lifted off from overworld, when you reached the height 1,200 your coord was X= 100, Z= 100, then the moon lander will spawn at X=100, Y=1,200, Z=100.
Solutions:
1) Simple one: Build the launch pad exactly at the same coord of the moon base's.
2) Interesting but might be impracticable: build a hub space station with a rail track to a launch pad built exactly at the moon base's coord. Player would need to land on this station and take a minecart to the launch pad.
3) This is for bold ones: players will be required to F3 and control manually the launch and "drive" the rocket to the coord of the moon base. If the moon base is at 1000,1000, the player would need to maneuver the rocket to 1000,1000 before exiting the overworld.
4) Economical: let them walk from wherever they land to the moon base.