As far as the slight imperfection of your shoe...
Personally, I don't think anyone would ever notice, and slight imperfections do occur with handmade shoes. As far as the color, polish or edge treatment will mask it, but that will do nothing about the shape. Still, I don't think anyone would ever notice that little miscut.
If they are not to your satisfaction, you always have the option of contacting AE or revisiting the store to find a flawless pair.
By the way, the walnut Strand is a beautiful first pair to grab. Well played, sir.