Hmm. One of the toughest issues with writing hypertext is this:
One does not communicate text. One communicates ideas.
Transclusion brings in an excerpt of text into an existing bit of writing. But it can't as a technique guarantee that the idea will still get across. In fact, another idea may be presented.
It's the difference between quoting and paraphrasing
Context is such a big part of meaning. It takes a different kind of thinking, a kind of humility to write hypertext. You have to give up some of the authorial power, admit that you can't form the perfect reader experience, and hand the power to the reader.
At the same time, you have to be twice as thoughtful, twice as controlling, just to make sure it doesn't flop.
To Win, Simply Play, by Dylan Kinnett, is a great little hypertext novella. When you read the novella, don't just think about what he does structurally. Think about the kinds of things he can and can't talk about. For example, chronology isn't a big part of the novella. Why not? Because he can't give the chronology direction, and anchoring stories to time would just force the reader to keep track.