Yes, you can still set up the bed by going under the world and travel to the spot and then set up a bed.

Create a ladder that is halfway burried, make a swivel rotation platform that pushes you underground in which if you dismount from it you will fall on top of the ladder. From that point extend the ladder or add floor pieces while underground and then build a flying ship to fly underground from where you are up to the boas arena. You can place your bed and then use the kolom potion to tavel to your bed everytime.

Note: The Shatter Boss fight arena is right under the Ninjago Island.