They do incur the cost of the tools and APIs. They would argue they eat the loss to support their market place.
I would argue apple making their APIs and tools open for everyone is in their best interests. It's easier to control security issues if everyone uses the same tools and apis. But apple won't care as much.
If a third party app store provides a tool or service to improve their app store, should apple expect to be able to use that for free? Negating any benefit that third party would get for developing such an improvement.