In isolated areas like Australia and Madagascar, species have filled nearly identical niches to the niches filled in much of the rest of the world, exactly as you'd expect from evolution, and not what we see human desigers do.

This isn't a great argument; human designers actually do this all the time. We call it "reinventing the wheel." We do it often when we're constrained against merely reusing parts of the same designs — for instance by copyright or personal pride.

Clearly the designer of the octopus eye was forbidden from just ganking the design of the mammalian eye, or vice versa. This is an argument for Semi-Intelligent Design By Committee, and thus for polytheism: the sea-god was either disallowed from copying the design done by the god of beasts, or was too damned proud to do so.