First up, I'm not bothered if my arguments are merely qualitative in your eyes. I am only "merely" doing metaphysics in the first place. So a lot of the time, my concern is about what the usual rush to quantification is missing. I'm not looking to add to science's reductionist kitset of simple models. I'm looking to highlight the backdrop holistic metaphysics that those kinds of models are usually collapsing.
And then a lot of your questions seem to revolve around your definition of degrees of freedom vs mine. It would be helpful if you explained what your definition actually is.
My definition is a metaphysically general one. So it is a little fuzzy, or broad, as you say.
To help you understand, I define degrees of freedom as dichotomous to constraints. So this is a systems science or hierarchy theory definition. I make the point that degrees of freedom are contextual. They are the definite directions of action that still remain for a system after the constraints of that system have suppressed or subtracted away all other possibilities.
So the normal reductionist metaphysical position is that degrees of freedom are just brute atomistic facts of some kind. But I seek to explain their existence. They are the definite possibilities for "actions in directions" that are left after constraints have had their effect. So degrees of freedom are local elements shaped by some global context, some backdrop history of a system's development.
Thus I have an actual metaphysical theory about degrees of freedom. Or rather, I think this to be the way that holists and hierarchy theorists think about them generally. Peirce would be the philosopher who really got it with his triadic system of semiosis. Degrees of freedom equate to his Secondness.
A second distinctive point is that I also follow semiotic thinkers in recognising an essential connection between Boltzmann entropy and Shannon uncertainty - the infodynamic view which Salthe expresses so well. So this is now a quantification of the qualitative argument I just gave. Now biosemiotics is moving towards the possibility of actual science.
Theoretical biologists and hierarchy theorists like Howard Pattee in particular have already created a general systems understanding of the mechanism by which life uses codes to harness entropy gradients. So the story of how information and dynamics relates via an "epistemic cut" has been around since the 1970s. It is the qualitative picture that led to evo-devo. And it is the devo aspect - the Prigogine-inspired self-organising story of dissipative structures - that has become cashed out in an abundance of quantitative models over the past 30 years. I assume you know all about dissipative structure theory.
So what we have is a view of life and mind that now is becoming firmly rooted in thermodynamics. Plus the "trick" that is semiotics, or the modelling relation.
The physico-chemical realm already wants to self-organise to dissipate energy flows more effectively. That in itself has been a small revolution in physical science. What you call configuration entropy would seem to be what I would call negentropy, or the degrees of freedom spent to create flow channelling structure - some system of constraints. And in the infodynamic (or pansemiotic) view, the negentropy is information. It is a habit of interpretance, to use Peirce's lingo. So we have the duality of entropy and information, or a sustaining flow of degrees of freedom and set of structuring constraints, at the heart of our most general thermodynamical description of nature.
Reductionist thinking usually just wants to talk about degrees of freedom and ignore the issue of how boundary conditions arise. The thermodynamics is basically already dead, gone to equilibrium, by the time anything is quantified. So the boundary conditions are taken as a given, not themselves emergently developed. For example, an ideal gas is contained in a rigid flask and sitting in a constant heat sink. Nothing can change or evolve in regard to the constraints that define the setting in which some bunch of non-interacting particles are free to blunder about like Newtonian billiard balls. But the dissipative structure view is all about how constraints can spontaneously self-organise. Order gets paid for if it is more effective at lowering the temperature of a system.
So thermodynamics itself is moving towards an entropy+information metaphysics. The mental shift I argue for is to see dissipative structure as not just merely a curiosity or exception to the rule, but instead the basic ontological story. As Layzer argues, the whole Big Bang universe is best understood as a dissipative structure. It is the "gone to equilibrium" Boltzmann statistical mechanics, the ideal gas story, that is the outlier so far as the real physical world is concerned. The focus of thermodynamics has to shift to one which sees the whole of a system developing. Just talking about the already developed system - the system that has ceased to change - is to miss what is actually core.
So physics itself is entropy+information in some deep way it is now exploring. And then biology is zeroing in on the actual semiotic machinery that both separates and connects the two to create the even more complex phenomenon of life and mind. So now we are talking about the epistemic cut, the creation of codes that symbolise information, capture it and remember it, so as to be able to construct the constraints needed to channel entropy flows. Rivers just carve channels in landscapes. Organisms can build paths using captured and internalised information.
Only recently, I believe the biosemiotic approach has made another huge step towards a quantitative understanding - one which I explained in detail here:
https://thephilosophyforum.com/discussion/comment/105999#Post_105999
So just as physics has focused on the Planck-scale as the way to unify entropy+information - find the one coin that measures both at a fundamental level - so biology might also have its own natural fundamental scale at the quasi-classical nanoscale (in a watery world). If you want to know what a biological degree of freedom looks like, it comes down to the unit of work that an ATP molecule can achieve as part of a cell's structural machinery.
To sum up, no doubt we have vastly different interests. You seem to be concerned with adding useful modelling tools to your reductionist kitbag. And so you view everything I might say through that lens.
But my motivation is far more general. I am interested in the qualitative arguments with which holism takes on reductionism. I am interested in the metaphysics that grounds the science. And where I seek to make contact with the quantitative is on the very issue of what counts as a proper act of measurement.
So yes, I am happy to talk loosely about degrees of freedom. It is a familiar enough term. And then I would define it more precisely in the spirit of systems science. I would point to how a local degree of freedom is contextually formed and so dichotomous to its "other" of some set of global constraints. Then further, I would point to the critical duality which now connects entropy and information as the two views of "a degree of freedom". So that step then brings life and its epistemic cut, its coding machinery, into the thermodynamics-based picture.
And then now I would highlight how biophysics is getting down to the business of cashing out the notion of a proper biological degree of freedom in some fundamental quantitative way. An ATP molecule as the cell's universal currency of work looks a good bet.
I'm sure you can already see in a hand-waving way how we might understand a rainforest's exergy in terms of the number of ATP molecules it can charge up per solar day. A mature forest would extract ATP even from the tiniest crumbs dropping off the table. A weedy forest clearing would not have the same digestive efficiency.
So I've tried to answer your questions carefully and plainly even though your questions were not particularly well posed. I hope you can respond in kind. And especially, accept that I just might not have the same research goals as you. To the degree my accounts are metaphysical and qualitative, I'm absolutely fine about that.