All the ports line up. The picture of the manifold you linked to is by design... universal. It will fit the PRB, RBB, RBC, RAA, and PPA cylinder heads. If you have the PRB head and need the water port... you would simply install the water neck. If you own any of the other heads... you simply plug it. This manifold may still exist in the market place but is no longer shipping from Skunk2.
Not to confuse the matter any further but to make everyone aware of some changes at Skunk2, Skunk2 has started chopping the universal water neck portion of the manifold off making a unique part number for the PRB guys.
The only other part number offered still keeps that cast in water neck but is only meant for the 06+ Civic Si customers. It has a throttle body flange specific to that application and is void of an IAC port. If you have a swap using that style head... you will need to buy a throttle body adaptor. If you want IAC function... you will need to port the manifold flange.