Waka 1 Skip
In Agata, the first Waka fight can be skipped with no consequences. The trigger permanently disappears if Ammy leaves Agata by going to Tsuta or Taka, so it doesn't interfere with later trips.
The trigger for the fight is too large to just jump around, but it can be avoided by KT'ing up to the ledge above the guardian sapling cave entrance.
With Brush Adventure
In NG, by performing a long brush adventure to bloom the cursed patch near Kokari, Ammy will be warped past the fight trigger. See https://youtu.be/iID96M7BhnE. Unfortunately, this loses approximately 10-15 seconds compared with simply fighting Waka, so it isn't done in any category.