If an effect causes a noncreature permanent to become a creature and sets its power and toughness as it does so, that creature will have that power and toughness; it won't be 3/3. Notably, crewing a Vehicle does not set its power and toughness, so a Vehicle will be a 3/3 creature once crewed.

Effects that modify a creature's power and/or toughness, such as the effect of Festive Funeral, will apply to the creature no matter when they started to take effect. The same is true for any counters that change its power and/or toughness.

Because damage remains marked on a creature until the damage is removed as the turn ends, nonlethal damage dealt to creatures may become lethal if Harmonious Archon enters or leaves the battlefield during that turn.

Harmonious Archon overwrites all previous effects that set a creature's base power and toughness to specific values. Any power- or toughness-setting effects that start to apply after Harmonious Archon enters the battlefield will overwrite this effect.