
I was pretty tempted to buy 1 of those tiger eye rock marbles

will make for a very awesome trackball & like you said will go with the walnut nicely, I really look forward to feeling confident enough to make my own custom peripherals like that, sweet modding quiz.
Maybe a simple brass plaque engraved would look better to cover the imperfection but I bet you could make that fit in place, it does look quite nice with the walnut, or a nice little simple pattern made from a different tone of veneer laid on top of the walnut. Just quick thoughts, not suggestions.