This may seem really dumb, but it kinda does have a purpose.
A clay tankard weighs a pound. A tankardful of ale weighs a pound.
Does that mean each clay tankard filled with ale weighs two pounds?
While it seems silly, and mundane, I can cast "Enhance Water", and I'm a drunken brute barbarian.
I want to know how much ale will fit into the main pouch of my handy haversack. How many rounds of rage max I can use in any given day.
Thanks :)
Weight in Pathfinder/D&D has always been a bit wonky. The reason for this (by my best guess) is that the game-term "weight" combines two things: how much mass something has, and how bloody hindering awkward it is to carry (how encumbering it is).
For extra-dimensional containers holding things with known mass (such as water having 1 pound per pint), use the real-world conversion. But for other containers, use their specific rules, if they have any. For the case of the waterskin, a 2 pound waterskin plus 4 pounds of water is (since the waterskin is explicitly designed to be easy to carry) considered to have an "encumbrance weight" of 4 pounds. A (possibly) good example is the grappling hook, which has a listed weight of 4 pounds. It's likely that the hook only masses 2-3 pounds, but because they're awkward to carry or hang from your belt or backpack, you use the listed weight. Weapons are another good case: most don't weight anything like the listed amount in the real world (for example, my heaviest kitchen knife (9 inch blade, 4 inch handle) weighs in at a whopping 6 1/2 oz, less than half that of a foot-long dagger, and yes I know about difference in design and purpose, but that's a heck of a weight difference).
It's this sort of thing that's the reason I'm quite comfortable telling my players that a rolled-up rug with a mass of 50 pounds encumbers in-game as 100 pounds.