Merge's discussion on webhooks and endpoints highlights their roles in application integration, defining webhooks as real-time data syncing methods where destination applications register endpoints in source applications to receive POST requests upon predefined events. Examples include creating invoices or updating ATS solutions through webhooks triggered by specific events. Endpoints, on the other hand, are API components presented as URLs that allow access to specific resources, as demonstrated by Stripe's and Sendoso's API endpoints. The text clarifies that while webhooks facilitate immediate data synchronization, endpoints serve as access points for APIs during requests. Merge's Unified API offers a platform for adding multiple integrations across software categories, emphasizing the importance of tooling for managing and maintaining customer integrations to ensure reliability.