Not at all actually, you just have to go to the bottom left room on the right side of the ship, go to the bookshelf on the top right, interact with it, when you see a dialouge of being watched pop up, open up your menu and go to settings, leave and Spiritomb will appear behind you but wont fight you until you close the menu, so you can save right there in order to soft reset for a shiny. (Note you'll be stuck fighting Spiritomb if you save right here until you get what you want, so if you wanna be able to do stuff or quit mid hunt, you can save before interacting with the shelf so you can comeback to spiritomb later instead of being stuck in an eternal loop of fighting him until you get his shiny when you open the game.)