The reason things are in line is due to the previous format forcing people to respond in order. Now that the outline format is back, you can reply to any reply you like, and it will indent as it had previously.
As for the numbering, it's that same as it was. I have no control over that. New threads do popup to the top though, and I thought we could try that out with this format for a while and see how it does. If it isn't liked either, it will also be removed.