I think your problem is related to the conditions the images are taken. The illumination is not even, and even this is not the same for both images. The camera may also be in cause (parameters of the white balance).
If I were you, I would to take new pictures, one for each apple at full resolution and closer distance. The illumination variations would probably be less problematic. It’s better to take good pictures than trying to process them to make them good.
If you cannot reproduce the images, you can at least take a picture of the background without apples, with exactly the same settings, then try to find a way to use it to correct the images (not sure how I would do that with color images, though).
But, if you really need to modify the images digitally now they’ve been taken, you can try Process>Subtract Background. Again, not sure how reliable the results will be.
One last point: If I zoom on the apples, they all don’t have the same texture, i.e. some of them are a little grainier/shinier than the others, possibly due to droplets of juice exsuding from the slice and the rugosity of the surface. I don’t know if it’s important, but be aware of that. If you take new pictures with one apple at a time, try to swipe it and check if it makes a difference. Also, be careful when quantifying the brown content: Don’t include the pips !
Useful tools : Analyze>Color histogram, Plugins>Color Inspector
Finally, if possible, don’t save images in JPG format (lossy format).