We've meanwhile added notes and other missing data to the JSON-LD output (the default export). The idea is that JSON-LD export covers all the information you add to an item in Tropy; we'll be using it to make copies or transfer items to other projects, so, naturally, all the information will stay covered.
We've also rolled out a plugin system for additional export formats (we're currently building a UI for managing plugin configurations that will go into the next release in a couple of weeks). Basically, an export plugin can register itself with Tropy; when you export items, it receives the respective JSON-LD data. At the moment there is an export plugin that uploads exported items to an Omeka server; we are also working on a plugin that takes the exported JSON-LD and saves it in an archive together with all the associated photos. It should be relatively easy to create a similar plugin that saves everything in a BagIt archive.
The plugin system is still evolving; we plan to make a richer API available to plugins as the need arises (e.g., to duplicate behavior already implemented in Tropy, like saving a selection from a photo) and also to allow plugins to hook into other aspects of Tropy (next on the list will be import plugins). My hope is that you'd be able to cover a range of use cases via the plugin system and would not need to fork the code base. In any case, I'm happy to answer any questions you might have here on the forums or on GitHub, just let me know!