One thing I'm wondering is how ATproto can be integrated with voice/video chat. Would you combine it with Matrix, XMPP, or some custom protocol?

One trick we've been playing with on the Matrix side is figuring out how to tunnel encrypted Matrix over other transports - so you could absolutely use it, layered on top of ATproto spaces, as a way to get E2EE DMLS metadata-protected realtime voice/video/chat but tied to ATproto DIDs and permissions. We're in the final stages of (at last) finalising MatrixRTC, the E2EE group voip stuff in Matrix, which would pair nicely with this.

The "portable Matrix" idea is currently nicknamed Tachyon, and is earlier stage at this point, although I did a Matrix Live about it a few months back: https://www.youtube.com/watch?v=jc7yfec3iIQ