To be honest I find day/night cycles fairly unimmersive just because the days and nights pass in the span of minutes while I've been watching my character move and talk in real time the whole time. I prefer this "the questing day is as long as you make it" strategy because I can imagine my characters being worn out after a couple big fights and wanting to rest the rest of the day.

The simplest way to fix the transition between the ship falling at night and the game beginning in the day is to just NOT have a falling animation when you hit the beach. Have you wake up. It implies you fell unconscious when the magic energy dropped you on your head.

Also the sense of urgency problem was largely fixed with Nettie getting a ton of new dialogue. She now explains to you that your tadpole isn't changing you and that it doesn't seem like it is going to change you for the foreseeable future, which informs you the player that you can take long rests more frequently.

It still isn't perfect because it seems like the game is designed assuming you rest before you ever meet Nettie, as meeting Nettie will trigger the Raphael scene and overwrite you making camp. But it is a big step toward smoothing out the gameplay vs narrative conflict the resting system creates.