First: I couldn't find a fitting Component for my Issue. I am very sorry, and hope you will read anyways and maybe change the component to one I couldn't see.

Story:

I think pictures will tell the story best:

The new sorting order for comments is counter intuitive. We read from top to bottom, not from bottom to top.

Also the button to reply is now as far away as possible. It would only be more difficult to reply if you hide the reply button on a second page or something.

Bonus:

The far far away reply button is grey.

Other buttons are strongly coloured and very close to the newest comment.

New users don't read and just click the closest strongly coloured button and then get confused.

Personal Opinion

I wonder If we are the only ones who find the new sorting wrong and the positioning of the reply button too far away. If you at Atlassian have tested this with your UX team and find it better for most of the people around the globe that I bow, but I doubt that.