That said, I don't think you should expect a Zulip-style threading user experience in Element anytime soon. Regardless of how the Matrix protocol for federation between servers is extended, providing the "Zulip user experience" would likely require a major overhaul of both their client/server protocol for Element and their client user experience. (Also, the proposal you link is for HN-style threading, not Zulip-style topics).
I don't understand Element's internals, but my basis for this claim is a huge portion of all technical and design work we do on Zulip wouldn't be necessary or would be much simpler if Zulip didn't have topics (E.g. the architectural decision criticized in https://news.ycombinator.com/item?id=27150492 is a good example). See https://news.ycombinator.com/item?id=27150196 for a few more examples. I imagine Element will only invest in all of that work that if they believe it's important to their business.
As an outside observer, Element's business focus seems to be on competing with WhatsApp/Messenger/Signal/Telegram/SMS, not Slack, so while I'd love to see Matrix/Element borrow Zulip's topics model, you probably shouldn't hold your breath.