I have an Aqara Thread over Matter smart lock too. The only thing I can do with it via Home Assistant is remote unlock/lock and get the battery %. I can't do user management or the million other features that require me to use the Aqara app.
Yes, that's true. I think Matter doesn't support yet many of additional configuration stuff. Hopefully that will change as the technology matures. As I use it with HomeKit as well I can do some user management through Apple Home. However, full config with all options only through BT and Aqara app, as you say. At least for now.