Hello, I'm new here, and to aikido, but this topic is something I've been giving quite a lot of thought to so it's prompted me to post my take, FWIW.
I don't think everything we see in aikido can be explained by physics, but I do suspect that, in theory, it's explicable by physics, neurophysiology, bio-mechanics and a number of other "hard science" disciplines working in conjunction. AFAIK this hasn't been done very comprehensively so far though. Big piece of work.
However, just because it's explicable within that paradigm doesn't mean there's no place for the use of the terms ki/chi or that they're not helpful. I see them as shorthand, metaphorical, poetic. Poetry condenses meaning and content in a more potent application of language than prose. If I say to my kids "weight underside" they get a lot harder to lift off the ground. If I had to explain to them what I meant in biomechanical and neurological terms they'd be "eh?" (and to be fair I wouldn't have much of an idea where to start).
There is a well-recognised paradox in that by deconstructing and analysing something we can also lose something of its essence whilst gaining understanding.
"oh! what a beautiful rainbow"
"oh, what an interesting splitting of white light into the spectrum through the refraction of sunlight by water droplets at the correct angle relative to me as an observer to produce this phenomenon"
Similarly, deconstructing a dance track into ABABAA structure in a major key with a 4/4 beat etc. doesn't help if you want to boogie your pants off.
Apparently there's been a resurgence of interest in metaphysics in the anglo-american tradition in the last couple of decades, not least amongst hard-nosed scientists and philosophers of science. I suppose physics is pretty damn weird when you really get into it and as a consequence people are growing more comfortable with questions along the lines of "what kind of stuff is there and what's it like?". An old friend from uni days who now teaches aikido and runs a philosophy faculty takes the line that "aikido is physics" but also that upon deep consideration all manifestation of physical existence in terms of "things" is illusory, there are no independent objects at all, everything comes down to structure and interrelationships. I don't understand this, or how it might be relevant, but offer it up because it sounds pretty cool.
According to some philosophers and scientists science does not explain anything at all, it gives a description of reality. Much like a recipe for an apple-pie. The recipe does not tell you anything about the sensation of eating the apple-pie or the taste of it. It only gives one description out of many of how you could make it.
There are still a lot of things that we cannot describe in a scientific way. Of many of these things we are totally unaware. Of some of it we are aware, but we find it hard to find words for it.
That is were poetry, metaphor, myths and stories come in. They have value to us in many different ways and can give us at times more comfort then science.
Being connected to nature is an important aspect of most budo. To me, living in the forests, this means in a very practical sense being aware of all the things that are happening in these forests, in other words being aware of the structure and the connectedness of everything.
I am surprised that your uni friend separates teaching Aikido from his understanding of how nature works? Combining these are for me the challenge.