I'm sure I'm not the first to have caught this.

http://www.imperial-library.info/obscure_text/cosmology.shtml tells us that the moons are not included in Dwarven Orreries. Why, then, is the Imperial Orrery entirely based on both? Is this just another hole courtesy of Oblivion? Or am I somehow misinterpereting this information?

could be the imperials were misconstruing the information.

Did Michael Kirkbride write the Cosmology article before or after the Orrery plugin was unveiled?

Well that would depend on the nature of the nomenclature of spells and abilities, and whether these are literal names given by the people of Nirn (in this case, the Mages' Guild) or whether the names are arbitrary.

At the time the Cosmology was written, there were no moons present in the Dwemer Orrery, that is Redguard's Orrery.

Well, it says Orreries in general, but your point is well taken.