The casting permission granted by The Indomitable's last ability doesn't change when you may cast it from your graveyard.

You still pay The Indomitable's costs when casting it from your graveyard.

If The Indomitable is countered or dies after being cast from your graveyard, it returns to the graveyard. It may be cast this way again later.

Once you begin casting a spell from your graveyard, it immediately moves to the stack. Players can't take any actions until you've finished casting the spell.

Only tapped Pirates and tapped Vehicles count toward the casting permission from The Indomitable's last ability.

The Indomitable checks if you control three or more tapped Pirates and/or Vehicles only as you begin to cast it. Once you begin to cast The Indomitable from your graveyard, it doesn't matter what happens to the tapped Pirates and/or Vehicles you control.