Some questions-
Who would govern these avatars and header graphics? The respective communities? If a community wants to set it to something the company doesn't like, what happens?
Any particular reason why challenges with domain names is mentioned? Are domains going to be removed? What about the link rot? Do cookies not work if a site was redirected to?
What about primary and secondary colours for a site?
What are the exceptions? I'm going to assume you're not going to simply let Stack Overflow's community change the avatar of Stack Overflow (at least- not without some sort of company review/approval process).
What does "unified features" mean? I assume from the framing that it involves tradeoffs. What things do you have in mind?
What will this mean for community-specific JS? Are you going to make it easier for sites to customize that through meta discussion and mod controls?