There is a new firmware available for the Eurotronic Spirit Zigbee thermostats that should help a lot on the problems seen with deconz. It actually works writing to them, and complain 
And the OTA file is now available here. But how do I get it inside the container. I can of course open a shell with portainer, but it doesn’t have something like scp or anything, so how do one do that?
Ok, I finally got some time to figure this out. By using the community add on of SSH, and not the official one, I could get this method to work: Update ZigBee firmware using deCONZ on Hass.io
So by doing that, the file is available for update from within deconz.