これは、改善できる簡単で汚いバージョンです。
from PIL import Image
from PIL import ImageChops
from PIL import ImageOps
import numpy as np
a = Image.open("a.png")
b = Image.open("b.png")
# Finds the difference between the two images. Then inverts so differences are black.
diff = ImageOps.invert(ImageChops.difference(a, b))
# Then we use numpy to convert black to red.
image = diff.convert('RGBA')
data = np.array(image)
r1,g1,b1 = 0,0,0
r2,g2,b2 = 255,0,0
red, green, blue = data[:,:,0], data[:,:,1], data[:,:,2]
mask = (red == r1) & (green == g1) & (blue == b1)
data[:,:,:3][mask] = [r2, g2, b2]
# Then we convert the array back to an image.
overlay = Image.fromarray(data)
# And blend with the original.
imgblend = ImageChops.add(a.convert('RGBA'), overlay,2)
imgblend.show()