Good questions.
I did 2+ years of chelation before beginning on methylation, so I'm pretty clear about what caused what.
I don't know that my body wasn't just improving on its own. But it hasn't for a long time. And it did - even in a new, unhealthy, high-stress culture (I moved to Cambodia); so I took a "best guess" that it was the methylation.
Also the methylation supps often have immediate good effects - you feel them same day, or same hour.
I also don't know that the whole thing isn't placebo. But I crudely "controlled" that by trying millions of other approaches over the years, which didn't do anything. That's the best I could do, as I can't afford much testing.
There are no RCTs on this because you can't patent most supplements. I was one of the first defenders of RCTs in the early 1980s; however since reading Dr Ben Goldacre's mega-tome on the corruption of the RCT process by drug companies, I no longer know (& therefore trust) what I am reading.
Yep, methylation protocols can definitely backfire tho. My initial effects (& the case reports from others) were so positive that I decided to work my way thru the crashes to find a formula that worked for me. The results are excellent but not perfect; & I won't be surprised if there are further crashes along the road.
The problem is you have simultaneously done a major chelation protocol. How do you know your feeling better is not attributable to that? How do you know your body wasn't just improving on its own?
It's very problematic that these methylation protocols have nearly zero double blind studies proving that they result in any positive health outcome. The people who do these protocols never carefully measure metabolites in a careful and controlled N=1 study to show what the total effect is on body chemistry. Everything is done based on subjective feelings which are subject to placebo effects and other outside variables (like doing a major chelation at the same time).
In my own case I tried methylation protocols, did carefully measure my metabolites before, during, and after, and all I succeeded in doing was increasing my metabolism in very dangerous ways that subjectively made me feel different but not better.