First, on 3 phase, drakes dps start at low damage and then increase as the time passed because of the DoT stacks, so CoE at the early doesn't give much bonus as CoE that lasts later on.
Second, there's nothing to prevent you from doing both
I'm not sure that debuff will be removed during his untargetable time between phase 2 and phase 3 or not, but you can try anyway.
Put CoE on him at the end of phase 1, if it's removed before phase 3 or duration ends before phase 3 ended, you can just do this afterward.