Thanks for your post! Hope you are well
Splitting the wall and removing the trim from that wall will be your best bet in this circumstance as the floor covering tool only does skirting, not cornice, so if you were to choose to not include the trim for all of your walls to spare your bathroom, you would only be able to add in skirting to the rest of your walls.
Also, for those internal walls, you can choose if you want trim on both sides or just 1 side (internal or external as shown when you draw the wall).
Hope this helps! Let me know if you have any further questions.