I don't think it is that bad. Have you already used Blackrocks? That usually makes things like that less noticeable. Most of the time, we aren't striving for perfection. Some patina is okay. It would be difficult to dye just those two spots, and if you end up covering the entire bag with some kind of colorant the texture of the leather will be compromised.
You could try the paint trick: Mix a little matching paint with a lot of conditioner and then blend it in. It usually works well for worn edges; not so much for random spots, but it might help a little.
I have had great success with Blackrock on vintage Coach Sonoma black pebbled leather. Like whateve mentioned, it can make light spots and scratches almost unnoticeable.
I bought a black Sonoma a few months ago that ended up having many light spots and scrapes on the side of the bag (see seller's pic of spots - hard to see tho). I was tempted to return it as they were worse in person than the picture showed, but the bag was so beautiful I decided to try rehabbing.
I washed the bag & conditioned with leather therapy (for the worst spots I did add a tiny bit of black acrylic artist's paint to the conditioner and applied to spots only & feathered out around spots). They looked better but were still noticeable.
But after applying Blackrock, all spots disappeared. I can't even find where they are now.
Great stuff (and great forum)! Hope this helps.