I can see some of the benefits of the integration: emacs can do the horizontal search for TODO entries, create an agenda, let you edit it, and move the changes to the right .org file. Still, I'd argue that the file is the important thing here, not the tool to manage it. I should be able to edit .org files with any other tool (e.g. an android app that eventually modifies a .org file in github), and then do re-process the file.

Other languages also allow exporting to other formats. I use md-to-pdf all the time, and it works well. Integrating the use of other tools in the export process should be independent of the usage of emacs.