If servers stay at a size that they can be handled by volunteer staff, I don't think you'll see defederation as any kind of normal thing to do. I think the worry is overblown.
Same as any other service, if you're willing to follow the rules of the stricter instance you can interact with it. If your instance won't abide by the stricter rules, so it goes.
I will be curious to see how it goes indeed. I hope the trend is a system of smaller instances with defederation fairly rare and with a tool that lets you at least manually interleave posts in magazines on different instances that you think should be in a single group. But this whole thing is not very old and I imagine in a year it will be very different.
I can't really think of any way to merge comment threads if multiple instances somehow shared a magazine despite having different mods. Can you imagine if half the comments in a thread vanished because a server shut down? I'm not sure that's even conceptually doable.
