While I have never seen a "functional medicine practitioner" this is roughly the same approach my doctor and I took 30 odd years ago when I was first diagnosed with Sarcoidosis, in addition to the Hashimoto's and polyarthritis I had for some time before that. We both wondered if there was a cause or trigger for all my various symptoms, so we went through a long (approximately 2 year if I remember correctly) process of elimination and reintroduction, meanwhile balancing and optimizing vitamin and trace element counts with supplements based on blood work.
We discovered that there was no particular food group that had any effect on me personally, either good or bad; but that on four separate occasions over the 2 years, Vitamin C supplements caused a serology reaction ( my ANA and inflammatory markers jumped).
I have also consulted a naturopath who was actually surprised to find that I didn't respond negatively to her testing for gluten and dairy, as it had been her experience that these triggers were quite common in inflammatory disease.
I have modified my diet for personal satisfaction, and eliminated imported, processed and refined foods. More of a lifestyle change than a health awareness one, and I've always enjoyed complex carbs over simple ones anyway, White bread? no way...give me something with flavour, substance and texture any day; and why on earth eat white sugar when I have access to MAPLE SYRUP?!