I had new dark brown Giannis from a couple years ago, and I removed a good amount of product by just vigorously buffing with a rag. You could do a bit more with VSC.It's not anything to be nervous about tampering with. At worst, the color underneath is less uniform - but I prefer that, actually.
Yes it's due to finishing. The dark cognac from Horween is not exactly uniform, and for better or worse, C&J applies finish to try to make it so. All my dark brown shell C&J has arrived with enough dark brown finish to soil one or two rags.