Yeah, you'd stack all the 5's into a single tower three dice high.
The way I determine the room is to add up the entire tower (in the example on the card it's 10+neighbors = 19). Then for things that neighbor the tower, I only count the specific dice that are physically in contact (so for the 3 die it only gets +5 from the tower).
However! It totally works either way you do it, it just shifts the results on the Room table up or down. So if you want more low results only count the top down view, if you want more high results count the entire merged rooms.