It makes it sound like the deal fell through but Sequoia still gave them $21M to be nice.
In reality, they had already given them the money in exchange for a board seat/equity/etc. When they realized they couldn't continue this relationship, the only option was to relinquish the half of the deal they could control. They probably couldn't get the money back even if they wanted to, and there's no way they'd attempt to and risk their reputation.
It makes sense for Sequoia and their LPs (Stanford, etc). They put $18 million into Stripe at a $100 million valuation, and Stripe is now worth $35Bn and growing. Sacrificing $21M to not hurt a relationship with Stripe is a rounding error for them.