ok, maybe what's different in my mind is that i am thinking about it as a phylogeny, that is, you have to look at what is primary before you can get to a given domain. set theory is founded on the fundamental topological concept of a manifold. you can't have a set without that first existing manifold.
imagine the universe just started. what is the first thing that is going to happen? space would be divided up. the shapes would evolve into more complex patterns, this is all topology.
set theory is after the fact. topology lets you start from really zero. then you divide it, and you start to see the beginnings of phyla of things, which you have to have before you can start talking about categorising, grouping, comparing and dividing them from each other.
yes, that's the key, dividing. dividing space, be it a surface or a line or a volume, is the fundamental basis of topology. the ways in which you do this form the first sets.
i still say topology is the root of all mathematics.
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We're gonna have to disagree out the gate. A manifold has a precise definition as a surface which is locally Reimanian, something like that. I'd classify it as one of the more elaborate constructs, and less primitive or whatever than a simple set. Afterall, you need set elements to talk about before you can define a manifold. All the formal stuff I've seen looks like "a group is a SET, with the following additional properties...".
Reading the rest I do see how you mean though, so I'll stop getting hung up on technical definitions. Yeah, I'd think patterns or differences come first, then the notion of distinct things. That's how I'm roughly understanding you.