Yes and no. It depends which branch of chemistry you world have chosen to go down. Physical Chemistry certainly improves a fair amount of the hand waving, but even there the underlying physics is simplified fairly often (as I understand it — I went straight Physics and dabbled in Chemistry from the other side).
Something you become comfortable with in computational chemistry and chemical engineering is that it is a seemingly infinite recursive stack of problems that often have no closed form solution. Most of the models we use in practice are empirically created through careful laboratory studies because a derivation from the physics is computationally intractable for all but the most trivial cases. This leads to phenomena like getting different numbers for the same thing depending on how you compute and derive them.
There are multiple approximate models for the same thing. Part of the skill is choosing a model likely to produce results that map closely to the real-world in a particular context with the least amount of effort. Chemical engineering as a discipline is effective at navigating and constraining the internal inconsistencies of these myriad models in a tractable way.
The sausage factory is real. There isn’t a tidy bit of theory or math under this that is useful in real settings. This partly explains the handwaving nature of the explanations if working in that sausage factory isn’t going to be your profession. Even if you wanted to understand the theoretical basis, that becomes extremely non-trivial very quickly, so it isn’t the kind of thing worth spending much time on if you aren’t going to go deep in it.
Not a satisfying answer, I know.
As a chemical engineer, one of the signs of maturity was myself and each of my classmates individually coming to accept and embrace the inevitable “magic coefficient”.
The curious always wanted to know why some magic coefficient was there. Where did it come from? How is it measured / calculated? How to derive the magic coefficient?
Eventually you learn that it’s turtles all the down. You can pick apart the magic coefficient and dive into the nuanced physics that its derived from…but then you still end up with a new magic coefficient.
So eventually, the curious students learn that the mysteries are out there for when you want to go out and explore them. But otherwise, we pick our level of abstraction for the problem we’re currently working on and accept the magic coefficients that apply to that level of abstraction.
The real trick is knowing the conditional boundaries when those magic coefficients no longed apply and you either need different ones or “here be dragons”.