I've frequently seen 3-4 'equivalent' posts in different instance's implementations of 'technology' (for instance) and the focus of the comments can be completely different. One on an infosec instance will have a completely different perspective than one on a Star Trek instance vs one on a completely generic instance, which leads to some interesting conversations that might get drowned out if everything were mixed together.
For me, I find this to be a large win and if it means I have to open 3-4 different threads, so be it.
That is what makes it hard. I often see the post in different communities with essentially the same discussion. That needs to be merged. However as you say it can also be in a different community with a different focus that shouldn't be.
Either you get fragmented theads where true conversation is stifled just by there not being enough people to talk to or you get too many people and the little niche conversations get drowned out and/or never happen.