I've seen some companies just take the total area (width x length x quantity) and multiply it by a constant that is chosen based on the number of layers, then add in extras like the solder mask color, etc. I have seen another company take the total area times a constant, plus the quantity times a constant, plus a setup fee. I've seen a third "PCB manufacturer" that just takes prices from the actual factory (and they have no idea how those prices are calculated), adds a profit margin, and rounds to the nearest ... whatever.
So it's all over the map.
- Bob