Here is the relevant passage.
"For every Grand Slam or mandatory ATP World Tour Masters 1000 tournament for which a player is not in the main draw, and was not (and, in the case of a Grand Slam, would not have been, had he and all other players entered) a main draw direct acceptance on the original acceptance list, and never became a main draw direct acceptance, the number of his results from all other eligible tournaments in the ranking period, that count for his ranking, is increased by one (1). Once a player is accepted in the main draw of one of these twelve (12) tournaments, as a direct acceptance, a qualifier, a special exempt or a lucky loser, or having accepted a wild card, his result in this tournament shall count for his ranking, whether or not he participates."
It is due to this that both Fed and Novak are able to count some other tournament in lieu of the
"mandatory" Miami and Madrid tourneys. The fact that they are not mandatory for people with exemptions are well known. What is new is their ability to substitute something else as long as they make sure not get on to the entry list at any point of time.