> make-whole. Verb. To restore (someone) to a sound, healthy, or otherwise favorable condition.

It's referring to their practice of boosting your per-delivery earnings to $6.85 if the customer does not tip you enough to meet that minimum payout.

A term you'll often hear wrt paying back creditors/investors/options, making them whole.

"To be made whole" means to fix a wrong doing, or restore something to the way it should be. They're saying they thought they were making it up to the employees when a customer didn't leave a tip. Which is just them trying to save face.