Wait, what?!
That seems like a pretty big flaw. Incoming transactions to a platform provider like Coinbase go to addresses that belong the the wallets of individuals. Once confirmed, they're then typically consolidated into shared wallets owned by the service, most of which should be offline.
When the customer send Bitcoin outside the platform, the actual address from which the coins are sent is arbitrary - it's just whichever storage wallet is currently hot. If, as a recipient, you send money back to the originating address, there is no way to figure out for certain which wallet on the platform it should go to. The money isn't "lost" - it's incorporated back into the hot wallet - but it's not routable to a customer within the platform.
In short, this seems like Stripe's fault. They should be assume that an overspend should be sent back to the address from which it came. There are all kinds of reasons this is a bad practice.