It relates to team composition and assault skill stacking. Once you have five same-element team members and around +40% assault skill modifier, neutral-element damage with your favored element outpaces the opposite element buff. In addition, your primary team will generally be better balanced (e.g., healing, debuffs) than an improvised opposite-element team.
You can check my DMG multiplier calculator (eidolon buff comparisons tab) to run the numbers on your own team.