You can cheese your way into saving in supernova by fast-traveling to The Unreliable, this creates an auto save point in the place you were, you'll just have to load it back again to continue. You'll have to endure some seconds of loading, but I think that's your best option.
Also you always save between loading screens, so just hop inside such doors and load the save again. You don't have to get back to your ship to save. And I also believe the game creates a save file when you exit, but I can't confirm that.
Saving limitations exists to make you think twice before facing some enemies, I have once come acoss two Mantiqueens and some Mantissaurs in the same group and I just left them alone and came back later after improving in gear and level. I did grown to like those limitations with time, they put the feeling of "I have a lot to lose risking that" into your heart.