I just noticed that in the latest version of Gaphor there's a floating toolbar on the canvas. I'm not sure this is a good fit in this case layout wise, especially at the top of the view near the headerbar it makes the layout feel unbalanced.

I could maybe see a case for having floating zoom buttons in the bottom right like in Loupe, but undo/redo and the alignment options would definitely be a better fit in the headerbar. My intuition would be to just move all of these controls into the headerbar on the left edge of the right panel.