intriguing subject, I hope I am not misunderstanding you.
In historical discussions here, it sometimes strikes me that there seems to be a notion that religious metaphor and practical advice are domains that can be separated for the historical topics discussed. Of course for us, that is the case, but I am not so sure it was for the historical figures. So when you say he was "honestly" talking about the gods, do you mean there was such separation in his own mind, or from our point of view in retrospect? If so, what makes you think that, in Ueshiba's world, there existed a division between practical IS training and religious metaphor? I am not asking this as a loaded or rhethorical question, btw.
One coudl argue that Tohei was just a later generation with a different (modernised) upbringing and cosmology.
In a similar vein, of course there is a philosophical position that metaphor (for some: should) be "reduced" to reality - there is also a strong argument, I find, that metaphor cannot always be reduced in such manner, that there are "absolute" metaphors (I take this from German philosopher Hans Blumenberg), and that philosophy and the history of science themeselves are full of important root metaphors (like "reading" nature, or the like).
Especially in relation to the experience of the body, I would tend to think myself that metaphor is irreducible. (Recently it was pointed out to me that a lot of body metaphors are apparently the result of synaesthesia, which again would be a facinating, different line of inquiry).
Just some points to start a discussion on a topic I find interesting - again, maybe based on a misunderstanding of the gist of your initial argument.
Well, in the 1990's I ran into the fact that hara/tanden/dantien is actually a functional thing that literally controls the body. So the dantien has a physical development. Did people find out about the physical development of the dantien before or after the dantien *after* the dantien had been postulated in theory and cosmology as something important? That would defy logic.
I found out that the body when trained correctly behaves along the lines of the "flow" diagrams in acupuncture/TCM.... coincidence? I think not. And there a more areas that accumulate and seem to solidify the idea that much of the things that appear to be the work of the vivid imagination of Taoist sages actually turn out to be totally in line with some real and demonstrable physical phenomena. The coincidence-after-the-fact idea crumbles under the weight.
What I think is that body-development along the practical physical qi/ki/prana/kokyu/shakti/jin lines could have long agao had a religious significance that was carried forward traditionally. So there would always have been an intermingling of religion and physical effect. It needs looking into because there's too much overlap for it all to just be coincidence.