This just looks strange.

More detail: The junk button in the expanded view isn't shown when messages are already marked as junk, when junk mail is disabled, or when looking at things like news. Its absence is conspicuous in the current layout. Consider moving it somewhere else.

Further detail: when the message has been marked as junk, the "Hide junk" button appears in the -- what is it called, Info Bar? -- that appears between the envelope and the body. This causes a strange jumping-around of the in-pane UI element that sets the status -- altho if you mark a message as junk, it will (typically) disappear as the message is moved off to the junk folder. Removing the button from the envelope panel entirely would be a better approach. The junk-status column in the thread pane (which, allowing you to mark the message as junk without opening it or even changing the selection), plus the toolbar-button for junk, should be sufficient.

Hmm, I am becoming dubious about just hiding the button, it might look better to remove the empty space. I believe I had concerns about the reply/forward buttons jumping around.

Well, somewhere along the line you did lose those concerns.