I'm personally against clonning communities as i think it's largely defragmenting already small communities into seperate little islands. The idea of federation is to create spaces where people can participate together no matter the instance they are from. Creating copies just goes against this idea IMO. One does not need to be on the isntance to participate in communities. That's the beauty of federation. I understand there might be reasons sometimes to do it, but if your idea is to just copy bunch of them so that you're the mod, I find it a waste.
As for disroot's branding of such communities. I think it would require admins to be part of the moderation of such community as it gives others the impression its related or at least supported endorsed by the team. Our idea for the instance was to make it more of a free for all approach then curated set of communities (eg. Beehav). So it makes sense that disroot branded communities are somewhat rated to disroot team or a project. At the same time other communities hosted on the server can use whatever branding they want.
So to sum up my position. I am rather against this idea. Using branding creates association for others. Even if you use disclaimers that it isn't. Since your communities are independent, I would rather see you create a unique branding to your comms so that people seeing them could straight away know who are they moderated and run by.
I think there were two reasons for that. One was that without centralized server where element could flash nunbers in front of VC there would not be much funding just like other open source protocols like xmpp experience. It also attracted more people because you didn't have to think of servers or bother with the whole federation concept (just join the main server, as everyone is there already).
Additionally matrix is pretty good distributed database but imo horrible chat protocol. It's extremely heavy on resources making other small servers impossible to compete or run on the same terms as the big ones. Back in the days I was running one of the top 5 size matrix server but I realized that the ever growing database, load issues when users joining large rooms and ton of other problems all, I went back to xmpp. It made me realized how crazy expensive and unsustainable in long run was running essentially text chat app became, and that could be better spent elewhere. Matrix is basically not designed for the purpose it's pushed for. It might be great as a communication platform in a organization or corporation or government agency ( you can accurately track the room state from its inception so great to have an overview of who, when, what). For fedi-like chat servers XMPP which can run on a potatoe is much better choice. Both from financial perspective (as your small server joining a big room does not affect you cause you don't need to replicate the room state essentially killing your server), but also environmental (its light and scales depending on your community needs better).