how does a PhD with no clinical experience bridge that gap?

I do not mean to suggest that the training a clinician receives is not useful for human health, rather that it is not as useful (no where near as useful) as it would be if the fundamental approach was one of biochemical physiology instead of... well, whatever it is. I'm not sure how I would qualify it, but its not that.

random bits of memorized information

This is kinda also my point. When diagnosing a problem with a car, a good mechanic starts from how a car works. It is much less knowledge based on memory, and more an understanding of the basic principles of function. The best mechanics are engineers. Of course diagnostics is a function of experience as much as functional understanding, but the functional understanding is necessary to really fix the problem.

As example with this analogy. Lets say I have a car that is running low on oil. The obvious fix is to add more oil. That doesn't in any way solve the problem (why the car is low on oil), but it will almost certainly keep the car running just fine. It could keep the car running just fine for a long time so we call that "a fix". Just keep buying more oil. Of course the problem persists and eventually the car will break, no matter how much oil you keep adding (how long you can keep spinning that plate).

In this analogy lets say its a worn ring that is causing the car to burn oil. Eventually that ring will cause enough cylinder wall damage that the engine will seize.

An engineer that saw low oil would begin diagnosing the real problem and, if they cared about the car, would have that engine apart by days end, breaking it down to check the rings and replace them.

Adding more oil is the approach of "medicine" all too often. That is because doctors are not engineers (just ask Bones). The fundamental knowledge of how each piece works separately and together (at multiple levels) changes the approach from one of ongoing treatment of a disease, to fixing the problem at the most basic level. A car can run indefinitely, but only if you understand the car at the physics, chemistry, and engineering level (even if just intuitively). The human body is the same.

Many doctors in my experience, unless they go outside of their core training to learn more and engage in real science, do not think critically, nor fundamentally about health. All of the fundamentals, the biochemical physiology critical thinking is handed off to the people who make the drugs. The doctors, for the most part, take these invested "scientists" at their word, because they lack sufficient knowledge, practice in real science, and discernment of data and analyses to do the critical thinking for themselves.

Doctors (sometimes) diagnose the basic problem fine in general (due in no small part to lab technicians), but then "Fix it" by handing out a prescription for an oil change. Maybe they throw in a car wash prescription as well; because hey, the pharmacology "experts" have it on their list as increasing the efficacy of the oil treatment.

When I was first getting to the part of my education where it was mostly coming from scientific research papers, I assumed that what was in the abstract and discussion sections was sufficient to understand the paper. As time went on and I digested more and more of the papers with less and less difficulty I found that what was in the plates was more important. The data, the pictures, the graphs; that told me pretty much everything I needed to know. From there I learned that what was in the abstract and discussion was very often biased, and sometimes completely untrue based on the rest of their presentation. Only someone who understands the basics intuitively can reach that level of discernment, and be critical of others work. It is that level of understanding of the workings of the body, the chemical physiology that is necessary to be able to prescribe the right things to fix the problem, not treat it.

We don't have the technology (that I am aware of) to fix every problem at this time, but we do have the knowledge of biochemistry (nutrition and other molecules), cell biology, tissue regeneration, etc. to fix a whole lot more than we currently do in "traditional medicine".

This problem was so glaring to me, I used to think it was just incompetence and stubbornness in upper management that created these traditions; "the ruling of the old guard." Now I think this tradition was created by the Cabal to keep us sick and dependent on their money making machine.