The way I was thinking you could still go to the original community and skip the aggregated one. So you could have c/gardening and c/flowers, but also c/backyard which could combine the two. You could still go to either one, but for easier discoverability you could create aggregators or include an aggregator in your community, and do this cross server. So if you have two very popular and overlapping communities you could combine them easier. Could also be a client feature I suppose. But right now you’d have to manually hunt for the possibly dispersed communities yourself. Alternatively I guess there is an argument for smaller communities being better which I do agree with. It was just a not very thought through idea :) Or you could have community redirects. So c/technology on lemmy.world could decide to seamlessly redirect to c/technology on Lemmy.ml if wanted. Edit: although the more I think about this the more it sounds like more trouble than it’s worth.
If the community is hosted on the defederated instance then I believe you wouldn’t see that post either. I believe the community instance reposts the post so that it can federate to all subscribed instances. And those might only be known to the instance that hosts the community. So everyone goes through it as a proxy.