This is an interesting topic but there's multiple questions here. I tried to write an answer, but even though I stayed very superficial, it ended being long. I gave up because I don't want to keep up with the maintenance of such a long post.

IMO this should be split into:

• How do I analyze the package inventory and dependency graph on my OS? (where you can talk about things like pactree)
• What is the architecture of a Linux system? (where you can do the taxonomy of DE, graphics server, systemd...)
• Can I swap out my DE? (you've picked an uncharacteristic example, most things like browsers or file managers obviously can be swapped, it's only the DE that's mysterious because "it starts on its own from the start so how could I possibly swap it")

Also, I feel like this invites the interjection. It would be better if the question sounded like it understands the difference between Linux and an OS, and maybe there could be another question like "Why do people say Linux is just the kernel, not the OS?" if it's really necessary.

The second of those questions is really what I was trying to get at. It honestly didn't occur to me that the DE would be "special" in this regard. The goal is to identify coherent components of the system - questions about swapping them could be separate, sure. What I meant about the package count is simply that there are a lot of packages, so I want to be able to think about groups of packages that make up comprehensible subsystems. I don't actually care about a dependency graph.

I more or less rewrote the question to try to express what I'm getting at more clearly. How does it look now?

Yeah, I think it's much better now.