I also think it's unusual that the layouts in the order we assume go BACK to the Throne Room for no explicable reason.
A while ago I looked at the layout orders and tried to see if any different one would make more sense than the one that is assumed. I think I remained inconclusive, but I do remember noticing that in order for the entire Throne Room's run to appear in consecutive layouts, the Troubled Bridge/Wheel would have needed to be taken down at some point before being put back up again, which I do not think they would go through the effort to do. As it is now, the Torch Room-Pirates' Cove-Room of Three Torches configuration makes the most sense.
EDIT: In fact, looking at it further, if any two layouts of the first season were to be switched in order, it would mess up the congruity of at least one room. (
this chart helps a lot to visualize that).