I've had some success dealing with this sort of problem with my antiquing.  I apply a lacquer resist and then apply and wipe off my antique.  This darkens all the leather a little bit, and it also leaves a little variation in the color of the untooled leather.  If you are careful about how you wipe it off, you can blend in the 'suntanned' areas a little bit and make them less noticeable.  It's even easier if that area happens to fall into a tooled area.

Here's an example of a custom notebook I've made, and as you look at the spine you can see a little variation in the coloring due to the antique.  Also where it has been backgrounded around the state of Texas the coloration varies a lot due to the texture of the backgrounding.  If you made a project where those marks are in a backgrounded or tooled area I doubt they would be visible once you were finished.  I've also had areas that are darker due to light exposure and I've cut out the leather so those lines end up around where my lacing holes will go.  Between the antique effects and the lacing I can't see the difference in coloration of the raw leather.front.jpg