More or less, yes - elements that are either indicative of a different phase being analyzed rather than the phase of interest (and thus not used in the sum normalization, yes; measuring Si to help better refine selection criteria for areas of carbonate minerals, for example), or for interference correction factors with certain mass numbers (where I got the "monitor element" term from - I've mostly seen this with older mass spectrometers).
I guess what I'm getting at is a way to control which elements or standards appear in in the secondary checks such that you can restrict the view to the elements or standards that matter most to that session, even if you're measuring other elements or standards.