Event Island doesn't change how those work in any way, so no, the game won't ignore your leader bonus because you're already getting a larger boost from the event; the event just won't give you a 200% and 75% bonus for the same bird anymore like it did back in the original (and decidedly not as good overall) version. If you're skeptical of that, note the listed amount of power the event interface tells you a team member that should get an additional bonus from the leader has prior to starting a battle, then tap on the bird in question during the battle to pull up the info screen (I recommend doing so when it is resting on the sidelines so you don't accidentally fire it in a non-optimal way), and you'll see that it's higher than the number it had before.