Quitting resets you to the spaceship?

When I quit the game to the menu and load the game again I experience that I'm back at the spaceship even though I saved at a checkpoint.

All the puzzles I solved are still solved, but my position is reset whenever I leave and reenters.
That's kinda annoying. Is it meant to be that way?

Due to the way Saira is a sprite and her parameters is initialized when the sprite is, it was simply easiest that way. Besides, if it works for Zelda...

Whatever puzzles you have solved/items you have acquired will remain, though.
Going back and forth on the planet by itself is really no problem, I think.