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.