I've built a couple tanks using the layout on the right, but it really doesn't matter. If done on the side the loss in structural strength is minimal since it was a low stress point to begin with. The overflow box will also add significant strength to notched part of the tank so it really doesn't matter which option you use. I'm not sure what your plans are for modifying your tank to incorporate this kind of overflow so do whatever is easiest.
Hard to see but,
You can also install an external overflow without notching the glass, drill a hole in the side of the tank and install two overflow boxes, one on each side. The one in the inside only needs to protrude about one inch so it won't really be noticeable. A much easier mod with similar results.