I thought pretty hard about it and I opted to make threads separate rooms because

1. parity: discord has separate things like permissions and pins for threads, matrix cannot do this at all unless the thread is a separate room
2. usage styles: most discord threads I've seen tend to be long-lived, spanning months or years, which isn't suited to matrix because of the timeline
  - I'm in a discord thread for posting photos of food that gets a couple posts a week and has a timeline going back to 2023
3. the timeline: if a matrix room has threads, and you want to scroll back through the timeline of a room OR of one of its threads, the timeline is merged, so you have to download every message linearised and throw them away if they aren't part of the thread you're looking through. it's bad for threads and it's bad for the main room
4. it is also very very complex for clients to implement read receipts and typing indicators correctly for the merged timeline. if your client doesn't implement this, or doesn't do it correctly, you have a bad experience. many clients don't. element seems to have done it well enough, but is an exception

overall in my view, threads-as-rooms has better parity and fewer downsides over native threads. but if there are things you don't like about this approach, I'm happy to discuss and see if we can improve them.