Both of the new screens look a magnitude improved and I'd be quite happy with either, also it looks plenty conventional to me, not much different from my GGale setup.
If you wanted a simple MDI without going with child windows you could use a simple split view system which could allow views of different canvases or multiple views of the same canvas. Even with a limitation of two panes you could have your reference image or preview in the spare pane, or have a DPaint/GrafX2 style zoom pane.
Even if you are to restrict the view to one image at a time it'd be nice to be able to have multiple images loaded and easily switch between them (that's how I usually work in MDIs anyway).
I think Kazuya's suggestion is more along the lines of what Pro Motion has (can't reach the site to get the name of the feature), where duplicated parts of the image (as delineated by the grid) are tracked and any change to one part propagates to all its duplicates, whereas I was suggesting an integrated tilemap editor (though I may have mentioned both). Either tool would be sufficient (both would be even better
). Pro Motion's solution should be easier to integrate into a straight paint tool however, needing no user interface beyond grid settings (which I'm sure you'll already have anyway) and a toggle.
I'm guessing from the "Layers" button that layer controls modally replace the "Box Options" panel. For me, I like my layers always at hand so: 1. I can tell that I'm editing the right layer; 2. I can easily toggle layer visibility; 3. I can easily switch the edit layer.
Nit-picky: for UI simplicity you could replace each of the box option pairs filled/unfilled, square/free, corner-to-corner/centre-to-corner with a single toggle button each.
I also put in my vote for themeable colouring.
