There is a great deal I wish to touch upon; what is it that you practice? Is it a Science? An art? What is the difference between the two?
Art would seem more ascetically based, insofar as the function is not necessarily the same as the elicitation of an effect on a subject, but more to the pleasing and expressing of an artistic nature.
Science seeks to cut away at the initial hypothesis and get the the root of truth contained there-in, whether it is confirmation of a hypothesis, or complete refutation of the same.
There can be no biased in the latter, while biased in the fore is really a non-issue insofar as one is not fooled by their own conception and can tell the difference.

I don't believe the two can be reconciled, but they can be practiced side by side as long as one keeps them in their respective positions.
If you practice for self-defense purposes, then the aim is functionality, however, perhaps a scientific approach, much the same as an artistic approach, is detrimental once it comes to effect.
Understanding the thing as a 'whole' is not possible considering the level at which the subject matter functions.
'Martial' implies 'War,' or 'Warrior,' the term 'Defense' also implies something of a confrontational or combative nature, even if we leave off the term 'Martial,' but that may be getting into semantics, which has a way of getting things sidetracked and missing the issue entirely.

The issue is only partially physiological, understanding how things function is mechanical, understanding physiological effects is a bonus, the other side of the coin, in order for the coin to be a true coin or a complete circle, is psychological, which carries with it all sorts of implications that often go over-looked in many places.
As such it cannot be understood in a normal logical fashion, but at the same time it can; so concretization and the creation of dogma only have a degrading effect on the study itself, which, like physics and psychology, cannot be differentiated from the observer or the observed, all the more true of our practice as Budoka, where one cannot separate oneself from that which is study because 'you' are a crucial part of that study... Which is violence, functioning wholely on a non-conscious, or semi-conscious level.

What is the difference between a technique, properly functional, with good solid power, and a punch, still properly function, good solid power, yet emotion backing it?
Ultimately different from a logical way of looking at things, from an intelligent way, had it anything to do with intelligence and reason at all it would not be necessary in the first place.
This is the realm of the unforgiving, unreasonable, highly emotional, volatile nature of humanity that has ensured the survival of countless generations.
Trial and error? Maybe, a strong possibility, but ultimately I feel it is something of an independent nature that can carry a person away and possess them entirely of its' own accord.
Perhaps the subject of study, as with some schools of Psychology, is reconciliation or a balancing act between the extremes, of conscious intelligent reasonableness, and this semi-conscious volatility.
It cannot be answered so easily, as Rory Miller says, the nature of violence is complicated and cannot truly be understood in its' entirety.

The point is not to kid ourselves, not to be overcome with bias, to open ourselves up, to be critical of what we do... In this way we grow.