Rulings

Mind Transfer Protocol overwrites all previous effects that set the creature or artifact's base power and toughness to specific values. Any power- or toughness-setting effects that start to apply afterward will overwrite this effect.
Effects that modify the creature's power and/or toughness, such as the effect of Karai's Technique, will apply to the creature no matter when they started to take effect. The same is true for counters that change its power and/or toughness and effects that switch its power and toughness.