In addition to their meta tags, Facebook also released an API that lets developers send Facebook a request with a URL to receive a response for the equivalent deeplink. This solution works best for deeper native integrations and those who want to go through Facebook to get this mapping. Fortunately, URX omnilinks already support Applink tags and don't require any code-level integration for developers to start linking to other apps.
Basically, the tags are open source (good), much like URX's working proposal [1], and the implementation of using the tags goes through Facebook. Facebook requires a native integration and does get around browser flashes, but is much more difficult to integrate than omnilinks, where you simply put urx.io/ in front of any weblink.