I have spent hours *ing myself on that matter.
Main-less teams works like in matsuri (items are rolled and "balanced"), only your main team has access to treasure tools and scrolls. BUT... the ninjas across the whole field keeps the stats gained through bonds. Exactly like matsuri.
I.e. if i have my edo tobirama team, in ranked my tobi will cast the barrier and my hiruzen in team 1 is able to cast his mystery. If i had another team equipped, i won't get my barrier and hiruzen will be interrupted by my kisame in team 3.
Okay, so basically the best thing to do would be to put whoever is going to hit hardest in your main team. Anyone else will just a balance work from RNG I suppose.
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