Hi Eliot,
Have I missed any other important considerations?
You got it right, both features are based on the same concept.
With the store module, your data is kept in main-memory until your BaseX instance is closed, so you can take full advantage of it in the context of server applications. It is not possible to keep multiple stores open at the same time, though. If you have contents that are related to specific databases, and if you have multiple users accessing your data, it is advisable to store them directly in the database.
If you create temporary data with BaseX and use it as a standalone tool, or if you work with a single user and a single database, it doesn’t make a big difference which feature you use.
Hope this helps, Christian