I think being skeptical (perhaps even cynical) is warranted. I don't recall how many doctors (conventional and alternative) I've seen over the past four-and-a-half years, but I stopped counting after a dozen.
Initially, I was pretty gung-ho about
Integrative/Functional Medicine doctors, as they claimed to "get to the root" of the problem and not just treat symptoms. But, after my own experience and observations, I now believe that much of "alternative" healthcare is simply about
escaping the collapsing conventional healthcare (sickcare) system.
Now, despite that last comment, many (certainly not all) alternative doctors probably believe in what they're doing. That is, they likely really believe all the expensive tests, expensive supplements, expensive therapies (HBOT, IV Vitamin C, FIR Sauna, etc.), restrictive diets, and recurring visits are going to make a difference.
But, as time has passed, I think some of the veteran Integrative/Functional Medicine doctors are starting to realize they don't have all the answers, either. The testing is neither all-encompassing nor perfect. Many are just as confused as we are, regarding diet. They tend to follow fads, like Paleo, Low-Carb, and, most recently, Ketogenic diets. Everyone has leaky gut and gluten sensitivity.
Rather than pharmaceutical medications, we swallow handfuls of supplements (fish oil, Vitamin D, etc.), in order to manage symptoms and manipulate biomarkers on lab tests, but still without addressing the root cause -- and, in the face of conflicting safety information and little-to-no conclusive evidence that any of this will lead to improved health outcomes over the long-term.
Thus, in my opinion, I don't believe that bowing-down to the altar of alternative medicine with unquestioning faith is any more of a viable strategy than blind faith in conventional medicine. Both can be useful and neither are perfect.
If I were to break a bone, I wouldn't want my doctor telling me to drink a cup of organic, shade-grown, mycotoxin-free coffee with grass-fed butter and MCT oil.* Rather, I'd want to go to the Emergency Room, get some pain medication, have the bone set, and a cast applied. Conversely, if I have a cough and the sniffles, I don't want an antibiotic. I'd rather try some elderberry syrup, hot baths, lots of rest, and reevaluate in a few days.
One of the best epiphanies I've had is that my doctors are consultants. I pay them for their professional opinion. However, my health is my own responsibility. So, I may follow their advice and I may not. In many cases, I realize they know much more than I do. In other cases, maybe not so much. I'm still trying to cultivate the ability to discern between the two, when it's not so obvious. And, getting a second opinion is always another option.
Now, since I'm not actively treating Lyme/Coinfections and have done little of it in the past, my above comments are general in nature and not necessarily aimed at Lyme-Literate Medical Doctors. Instead, the above harangue is just how I feel about my experience in alternative healthcare, in general. And, it's just an opinion. I'm not claiming to be correct. 
__________
*Actually, if any doctor ever suggested this, under any circumstances, it would be time to find a new doctor.