In-so-far as the rules serve to describe how the setting works and what is possible in the setting, I prefer they go first. But only those rules necessary to adequately describe the setting when the setting in question is tied to a previously published game. When dealing with a game with an explicit setting then the rules should be as comprehensive as possible.
For instance, if the game your setting is tied to has one mechanic for computer use, and computers work differently in your setting, then a modified computer use mechanic would be appropriate. But be sure to include a notification that the setting's computer use rules take precedence over the core rules'.
For instance, if the game your setting is tied to has one mechanic for computer use, and computers work differently in your setting, then a modified computer use mechanic would be appropriate. But be sure to include a notification that the setting's computer use rules take precedence over the core rules'.