Yes, the MCU of ConBee II and RaspBee II can drive the Thread protocol. There is a port of OpenThread for the this platform (SAM R21).
So this combined with the open Matter implementation should work to connect to these networks.
I haven’t tested this yet as there are currently no products available for Matter (I think the first ones come out this year if not delayed again).
Thread is completely different from Zigbee, which unfortunately means you can’t run both on one ConBee II at the same time. I’m not sure yet if Matter will be integrated directly to deCONZ or if it will be a different application. However from the REST API perspective I think it makes sense that both are are accessible over the same REST API, meaning that clients which talk to current deCONZ REST API get access to Matter devices without changes. Of course this is currently all just theory and needs to be evaluated in practice.
Beside the current REST API I’d like to turn deCONZ or a companion application to implement a Zigbee <–> Matter bridge (like the Hue bridge does). To expose our already existing Zigbee devices to Matter clients, this would be pretty cool so that for example HomeKit, Google, Alexa and Co can talk to these devices over a common API.
However I’m not sure if this will be possible at all, since the Matter specification is filled with many walled garden “features”, so that clients can check and reject devices which aren’t officially marked “worthy” — this is the ugly part of Matter which the marketing is very silent about.