The extra space above the Reply button isn’t intentional. We can surely tidy that up.
The extra space around the diff is sort of almost an illusion, kinda. It’s really space allocated for the diff header/footer/expansion controls, but we use some CSS magic to squash those so that we can slide then back into position when hovering over the diff, without impacting layout on the page. In 2.5, hovering would expand and push page content down, which slowed down the page briefly and made scrolling pretty rough whenever the page scroll caused the cursor to land over the diff. The header needs to expand into its allocated position on the page, which is why that gap is there.
The one at the top though is completely fixable, so we’ll poke at that.