Apply schema defaults after refinements

Currently, Astro config defaults are defined in https://github.com/withastro/astro/blob/c8ac8e5eed7fa8db7111878ada787243cedc09b7/packages/astro/src/core/config/schemas/base.ts. The problem this way is that they apply too early, before integrations. We must find a way to apply defaults after `astro:config:setup` ran for all integrations. We also need to see how that impacts types.