I guess this is a big undertaking, but I open this bug/feature request to be present on the tracker as I haven't seen such issue. Personal opinion: the way nheko does it is quite useful and not so obtrusive, one cannot miss a message, when tracking the full msg timeline, however the element/slack way helps by hiding the threaded messages from the timeline. I wish for something that makes it easy to realize I have to check threads, however hides it from the timeline.
This is something we have on are radar and is already in our internal issue tracker https://invent.kde.org/network/neochat/-/issues/561.
any news about that? it's an important and useful feature at the moment I use nheko.. it solve this semi optimal.. Element also.. a good solution for that has rocket.chat, in thread answers has an smaller font size, than you can answer inline or klick on it and answer in an extra window where you see just the thread
Making progress, master currently has some of the base functionality behind a feature flag and I'm working on getting everything I need for a good experience sorted.