Mac OSX 10.12.1
2.8 Ghz Intel Core i7
AMD Radeon R9 M370x 2048GB
Stock Launcher Unmodified
4GB RAM Allocated
When changing the "Depth Base Size" and "Sea Level" to double their defaults (17 and 126 respectively) only certain structures spawn incorrectly.
Dungeons, Strongholds, Witch huts, Villages, Mansions, and Igloos spawn correctly (no more or less different than normal).
However Ocean Monuments and Desert temples appear to fail to adjust to the difference in base height. Desert Temples spawn underground and Ocean Monuments cut into the sea floor leaving a cliff around them do to the sea floor being approximately 20 to 25 blocks higher than default.
I believe this to be a bug due to it only affecting select structures. I have included screenshots of the structures as well as one of a village that spawns normally. The F3 screen is open so that you can observe might Y level in the world. I have no info at this time as to whether Jungle Temples are effected I have not been able to locate one.