In the July 4th issue of Jinja Shinpō, there was an article about Nantai Jinja in Ibaraki Prefecture. The article was mainly about a ceremony performed to mark Mt Nantai being opened for mountain climbing after the winter (such ceremonies are fairly common), and the notes on the jinja and its kami at the end were interesting.
The notes start by saying that Mt Nantai, because it is also visible from the Pacific Ocean, is venerated as a kami of farming and fishing. It then says that Nantai Jinja enshrines Izanagi-no-Mikoto, who is venerated on Mt Nantai, and Izanami-no-Mikoto, who is venerated on Mt Nyotai, which is next to it. The chief priest of Nantai Jinja, Revd Kikuchi, said that Mt Nantai was always watching over their daily lives, and that it had a shape suitable to a “spirit mountain”.
So, is the mountain itself the kami, or is it a place where one of the main kami from the ancient myths resides? The answer is, almost certainly, “both”. “Nantai” means “male body”, while “nyotai” means “female body”, and pairs of Mt Nantai and Mt Nyotai are not uncommon in Japan. (Indeed, that is why I am fairly confident about my reading of the names.) If you have a pair of mountains venerated as embodiments of a man and a woman, then associating them with the most prominent male/female pair in the myths, Izanagi and Izanami, is not a difficult leap to make. Thus, both practices could easily have existed in the same place. In the Meiji period, jinja were strongly encouraged to identify their kami with named kami from the Kojiki or Nihonshoki, which might have been the final push for the jinja to firmly identify its kami with Izanagi and Izanami, while beliefs about the mountains remained less settled.
That is pure speculation, but the veneration of both the mountain, and of a kami who is resident there, is a feature of Shinto practice that can also be found at a number of other sites in Japan.