Bonuses to GPS or Coin value will apply to challenge rewards for any challenge accessed from the challenge page in-game. However, after beating that first challenge, pressing the "next challenge" button to continue using keys will prevent buffs, like those from Firefly Events, from applying to that challenge's gold rewards.
#Firefly Event Buffs Not Applying When Moving Straight To Next Challenge
open imp
open imp
Update: This also seems to hold true for pet bonuses!