Generally speaking in the context of meth as a street drug “crystal” meth is the purer form of meth, compared to other illicit preparations. It is called “crystal” because of the formation of large Meth HCl crystals, which only form when the concentration of meth in the solution being precipitated is high. Otherwise you get a powder of the same substance, generally at a lower purity. Crystal is still likely to be a racemic mixture of L/D-meth with various impurities, but fewer impurities than other forms made in the wild. By contrast Desoxyn (the pill you mention) is pure D-meth, which is far more potent than L-meth or a racemic mixture. You will almost never find enantiomerically pure meth outside of the context of Desoxyn, so in fact crystal meth is not, “the same as prescription pharmaceutical pills” because the legal, Rx form is markedly stronger.
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.