I suspect that one or two instances will eventually contain all popular communities
I definitely agree. It's so much easier to find communities within your own instance, thus communities on large instances automatically have an advantage over communities on smaller instances. I'm currently having this issue with a community I moderate on lemmy.ml that isn't even showing up on searches across the fediverse
I would imagine it working just like on reddit and lemmy, where it can originally be claimed by the original poster or anyone who wants it. It's obviously not an ideal solution, but it's worked well enough historically. Maybe someone else would have a better idea