Point 1 and 4 are key for maximizing efficiency.

In the old version with reply box at the top and comments below, newest first, your eye can always go to the top and action what's there. In the new version with comments oldest first and the reply box at the bottom, your eyes have to go all over the screen to find where the latest comment is (a one comment ticket will have the comment at the top, one with many tickets have the comments at the bottom, others somewhere in the middle), then from there find where the reply box is to answer.

The new layout requires a lot more effort just finding the content to reply to, rather than being able to rely on it always being at the same spot on the screen. It also defeats the purpose of larger screens as on any short tickets the reply box is very far away from the comment you're reading.

Sure, your agents can get used to a less efficient flow, but that doesn't mean it's ideal.