Using stuff to remove stuff before applying other stuff seems rather unnecessary. Brush the damn things, and wear them. If there's any excess polish or finish on them, it will wear away just fine.
Anyway, going back to the OP's main issue, that one part of the shoe was a different colour to the rest, that's just the natura of the beast. And removing the finish will probably emphasise the variation rather than reduce it. Shells do not have even colour; that's part of the charm. And with a mass produced shoe, it might well not even have been from the same shell. Horween's "Colour 8" varies from dark oxblood to port wine to quite a bright bloody red. Every shell is different. Learn to love it.
Ah! You just addressed your concern within your own quotes. Look, they tried to even out the difference in color. But guess what, they dumped truck loads of inks on the surface. Now, what does sticky surface inks do that we are all trying so hard to avoid? Brushing isn't going to help, and the application of a better product is more than necessary. If it's excess polish, who cares? But, it isn't.
The difference in coloration is all due to different lighting. Hell, even the shine varies from the left boot/shoe to the right.