You may already know this, but I think this is what you are noticing:
"As some people have heard or read, the “lighter” and “darker” colors of cordovan are that way for a reason. The leather, being a unique medium, has highs and lows in terms of natural color. The darker shells are many times that way because this makes for the most uniform finished product. As our shells are stained with fully aniline stains (meaning no pigment to provide coverage of any kind), fading your darker colored shells may cause these color “differences” to become detectable, if they even exist at all."
I think that if you get them refinished by Alden or B. Nelson, the inconsistency will be hidden again. Or as was suggested, use saphir cordovan cream (which contains a lot of pigment) to cover it up, but it will likely darken the color of the boot back to close to its original color. IME, Saphir cordovan cream can't be used to spot treat, as there will be a visible difference between the treated and un-treated area. You have to use it on the entire/shoe boot.
Bakes, I actually hadn't read that but it makes a lot of sense and is very likely what I am experiencing. I think I am going to try to live with the spot as Uncle recommends and see if it becomes more pronounced as the leather lightens further. If that happens, then I might consider some remedy options. Thanks much for enlightening me.