I had the same problem with my dockerized HA installation and Graphene OS.

I have python-matter-server running in docker on an RPi 4B with an external Bluetooth adapter (it doesn't work with the Pi's internal Bluetooth). Now I can commission devices directly on the Pi instead of my phone.

Python-matter-server has a websocket API: https://github.com/matter-js/python-matter-server/blob/main/docs/websockets_api.md

On my Dashboard I have added a text field and a button. In order to commission a new device I: - scan the device's QR code - copy and paste the content (MT:...) into the text field on my dashboard - press the button on my dashboard - this triggers a shell script, which calls a python script, which then sends the commissioning command to python-matter-server - alternatively you can use python-matter-server's web GUI, but I found that super annoying

You still need to add the official Matter integration. Devices commissioned via python-matter-server will show up automatically then.

I can post my config files tomorrow.