We have been playing that the number of board expansions does not effect the successes required to defeat the elder god, as it does not seem in the spirit of the rule. The rules seem to back this up but do not explicitly state it.
Successes Required to Defeat the Elder God: When the Elder God wakes the number of successes is set to the number of Players(I take this to mean agents if some players are playing more then 1) times the number of spaces elder gods doom track.
Combining Multiple Expansions: "The rules are unchanged when using more than one expansion city, except that the number of players should be counted as being one less for each expansion board in play beyond the first. So, if six players are playing a game using both Dunwich and Innsmouth (for a total of two expansion cities), they are counted as having one less player, for a total of five players. This modified number of players is used for such things as the monster limit and the maximum number of gates that can be open at once, and it reduces the level of difficulty for the players since they have so much more ground to cover"