The Persist Creature does not have a -1/-1 counter on it.
You control your commander.
Steps
Activate
Bartolomé del Presidio by sacrificing the Persist Creature.
When the Persist Creature dies, it triggers, returning it from your graveyard to the battlefield without a -1/-1 counter on it due to your commander's ability granted to it by
Master Chef.
Resolve the
Bartolomé del Presidio ability, putting a +1/+1 counter on it.