In short, you’ve ignored both the issues of impurities and cutting agents in illegal meth, and the important stereochemistry.
The issue of mentioning MDMA, while it may offend your sensibilities, does make sense in terms of being in the same family as methamphetamine and amphetamine. They do have different effects, but they share a similar chemistry.
http://www.emcdda.europa.eu/publications/eu-drug-markets/201...
In addition both substituted amphetamines seem to be neurotoxic in similar ways. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3231568/
The difference in outcomes between meth and MDMA abuse may well have more to do with typical patterns of use and abuse rather than a fundamental difference in pharmacokinetics. If you’re going to feel as you put it, “triggered” by an article at least be so as a result of valid concerns based on the science.