The rules in Mu are a little unspecified here, but the way that I have handled it is that the 1-3 bonus can be used once. Of course the cumulative successes rule applies, so those dice can help beyond just Contacting (if that's the point they are used in), but I think adding them into every single roll as a given bonus gets too extraneous.
That said, I tend to be a little generous with my bonus dice, and thus have no complications giving out extra 1-3 bonus dice per cross-referenced dictionary item. Obviously if players are just going through the book halfheartedly do not award them anything, but I think any amount of tieing the situation to the setting deserves an award.