"You should realize at the outset that while knowing about the internals of Mathematica may be of intellectual interest, it is usually much less important in practice than you might at first suppose. Indeed, in almost all practical uses of Mathematica, issues about how Mathematica works inside turn out to be largely irrelevant. Particularly in more advanced applications of Mathematica, it may sometimes seem worthwhile to try to analyze internal algorithms in order to predict which way of doing a given computation will be the most efficient. But most often the analyses will not be worthwhile. For the internals of Mathematica are quite complicated."
Reference: http://reference.wolfram.com/language/tutorial/WhyYouDoNotUs...
For comparison, if you want to audit the Sage Math algorithms that your research depends upon, all you need to do is fire up a text editor (or browse their github). And you won't find any statement in the Sage Math docs telling you not to bother because you're too dumb to understand what you're reading anyway.