I have noticed that with terrain control, the default structures like desert temples or jungle temples dont spawn in their own biome...
Here is an example:
http://oi60.tinypic.com/34nr7o2.jpg

I noticed an option at each biome config. i can turn off the structures from the sea, like in this pic where the desert structure spawned in the ocean biome. But i have also noticed a jungle temple inside a desert biome :/
i believe the opposite is possible

I found in the biome configuration:

The type of the aboveground rare building in this biome. Can be desertPyramid, jungleTemple, swampHut or disabled.

RareBuildingType: desertPyramid
its ok close the ticket.

feels self enlightenment... i like it!

Closing as requested.

I wonder how the pyramid got there. In the default settings there aren't any pyramids in oceans.