I must have been playing with fire for, well, since ever then. :DDon't just land on a planet and get out. Clipping issues, gravity issues, physics issues, these are all things that make this a very bad idea.
Pro Tip: Early on when you can't afford a station yet, put a shop block in your ground base so that you can access blueprints. If your ship is too big to bring near a planet (more than about 1k mass), deconstruct the ship and store the blocks in your blueprint, then take a 3 block pod down to your base. When you're ready to leave, take the pod back up and then respawn the ship in orbit.I'm glad I read this thread yesterday. I parked my first starter ship in orbit instead of on the planet just so I don't run into this. I'll have to figure out rail docking this weekend.