This has always bothered me a little bit, for example when talking about "electrophilic aromatic substitution", the untrained chemist might presume this meant the aromatic system acting as an electrophile, and vice-versa for SnAr. It's a semantic issue I suppose, but I can see why people get confused. Arbitrarily separating your reaction into "substrate" and "reagent" seems a little bit dodgy to me though, from the mechanism's point of view there is no difference between your late-stage alkaloid precursor and the methyl iodide you're using to methylate it. Also, one could imagine a convergent natural product synthesis where the two fragments come together, one as an electrophile and one as a nucleophile...