The one thing buff might affect is shield/confidence(wind blade asuma)
if w/o buff, your shield breaks before the end, you might do lower damage than expected, because you lose the confidence buff.
other than that, I do believe buff will affect all teams equally.
What is really troubling is the effect of mood and awaken can have, because it's unrealistic for one to have all potential ninjas mooded and max awakened (awaken mat at higher level is difficult, due to large requirement), which means your existing "polished" team with mood and max awaken might do more damage because of those factors as opposed to the team being superior. Of course, if the damage increase is minor (say from 0.40% to 0.40001% damage per attack), maybe it's not worth switching due to the investment already made, but a clearer view of exactly how much better a team is compared to another is very important.