I have my own method for dealing with this syndrome. If you choose to try it, pease do so at your own risk.
What I do is use KIWI creme polish. I open the jar, and squueze a dollop of leather lotion (conditioner) in the centre of the creme. then with a finger I start gently mixing the polish into the lotion, creating a well of the new mix in the center of the jar.
Once I've mixed this 50-50 lotion-polish, I take a small amount on my finger and start working it into the leather.
The lotion dilutes the creme, and also extends the drying time of the creme. This gives me more time to fine tune to my liking where and how I apply polish creme. Wih the markings on your shoes, this tecnique will tone down the blothciness and give depth to the finish.
A little polish-otion goes a long way as you will see that by applying only thin coats with your finger, you will achieve some very pleasing results. To sum it up, this method will work with the blotches rather than outrightly trying to hide them, and I feel this is what adds to the character of the finish.
Once the applied mix is thoroughly dry (1 hour), I follow with a medium brown wax polish on the to caps only jut to further deepen the finish.
Dry, then brush, then buff with a soft flannel cloth. The final resul should be somewherein the dark chestnut area.
I would also like to see other members ring in on this with their suggestions.
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