Not trying to argue, but this is not much of discoloration but rather marks left from running dyes. Alden finish their dark color shell shoes with liquid dyes, as a way to even out the color variations and imperfections inherent in shell Cordovan. Frequently, the application of the dye is not perfectly even, leaving behind these marks.
Examine a few pairs of dark color shell Alden in very strong light (e.g. direct sun light), and you should see varying degrees of imperfections.
I am not saying that it is acceptable. Ultimately, it is the consumer's decision. BTW, an alternative option is to complain directly to Alden. I am pretty sure they will fix the issue for free, by applying more dyes to cover up the marks.
I appreciate your explanation of the process. I guess I have been lucky over the years: I have never run into this despite seeing and owning a number of pair of color 8 cordovan shoes. Running dye or discoloration, the process in this instance lead to a notable result in this particular pair of shoes.