Because having communities with an identical name on different instances will fracture the community.
They're different communities on different websites, though. Trying to force them all into one space is erasing all communities but one, just for the sake of having to see an @website.com address, or for pretending you're not missing out on something when you ignore 99.9% of posts and comments that end up in the space.
1 million users discussing a topic spread out across 1000 communities of 1000 active users leads to more vibrant and meaningful discussions on that topic than having 1 million of them all crammed into one place, shouting and competing for slivers of attention. And no one will miss anything of deep value in the 999 other communities, because people will cross-post the good bits anyway.