This right here. The primary benefit of the matrix protocol would be that a community would keep on chugging as any particular instances go up and down. There would be no "home" instance that goes down and takes the community with it.
This choice is going to see some communities get really big, but then the "home" instance goes belly-up, or makes some, ahem "management decisions" that really hurt the community, and they are going to have to painfully jump ship again and again.
The downside would be higher resource demands for instance owners -but that's a problem that will get better over time, instead of worse.
The resource issue also isn't really that big of a deal, i've managed to keep up with tons of big chat rooms with messages every second on my OLD matrix server, and it's been refined since then.