The hard realization here is that the "General Consensus" is not always based on scientific fact, and the "evidence-base" assumed to be of "value" may turn out to be false.  Likewise, some of the "non-traditional" therapies do have "evidence" and scientific merit, however the average practitioner may not have the time or knowledge base to either drill down to it, or understand it.

For example the controversy regarding homocysteine.  The popular internet medical resource "UPtoDate" reflects your opinion that treating homocysteine is not indicated based on scientific trials.  Please refer to the following review from the European Heart Journal for another perspective:

from folate fortification to the recent clinical trials,  European Heart Journal (2009) 30, 6–15.

Are there some clinical circumstances where the benefit outweighs the risks, or where the benefit is possible and the risk unlikely (perhaps except for cost of screening and cost of the supplment), is it unreasonable, particularly if the patient is willing to bear "the cost". 

It is now recognized that vitamin D is a hormone with multiple interactions in  biochemical and metabolic pathways exerting influence outside of bone metabolism, including diabetes.  Vitmain E has different formulations.  Are our conclusions about Vitamin E concerning all varieties?  The same can be said about the effects of estrogens in women.  Is the biochemical and hormonal effect  from a melange of molecules obtained from horse urine the same as the "bioidentical" hormone? Heart failure has been described as a multiple endocrine disorder, and testosterone is now being proposed to have a role as well.  These have all been included in the realm of "non-traditional" medicine.  What really is the science?

What you explain as "Naturopathic" remedies may be, and sometimes are legitimate therapies.  And some of our "evidence based therapies", are just wrong, based on poor trial design, implementation, or as has been shown, unethical conflict of interest.

Lets face it, we can't  agree on what to tell our patients  to eat (low fat, vegetarian, low glycemic, or low carb) when they are obese, dyslipidemic, or diabetic. 

Each physician has an obligation to his patient, which we all feel is an honor and privilege.  Before we criticize another practitioners "art and practice of medicine" (and this is where our patients get their information) we must examine our own first.  Sometimes by virtue of our own training and experience, our perceptions are altered, which interfere with our ability to best serve our patients.