Edit image pixel by pixel - Python

I renamed your images according to my way of thinking, so I took this as image.png:

and this as mask.png:

Then I did what I think you want as follows. I wrote it quite verbosely so you can see all the steps along the way:

#!/usr/local/bin/python3
from PIL import Image
import numpy as np

# Open input images
image = Image.open("image.png")
mask  = Image.open("mask.png")

# Get dimensions
h,w=image.size

# Resize mask to match image, taking care not to introduce new colours (Image.NEAREST)
mask = mask.resize((h,w), Image.NEAREST)    
mask.save('mask_resized.png')

# Convert both images to numpy equivalents
npimage = np.array(image)
npmask  = np.array(mask)

# Make image transparent where mask is not blue
# Blue pixels in mask seem to show up as RGB(163 204 255)
npimage[:,:,3] = np.where((npmask[:,:,0]<170) & (npmask[:,:,1]<210) & (npmask[:,:,2]>250),255,0).astype(np.uint8)

# Identify grey pixels in image, i.e. R=G=B, and make transparent also
RequalsG=np.where(npimage[:,:,0]==npimage[:,:,1],1,0)
RequalsB=np.where(npimage[:,:,0]==npimage[:,:,2],1,0)
grey=(RequalsG*RequalsB).astype(np.uint8)
npimage[:,:,3] *= 1-grey

# Convert numpy image to PIL image and save
PILrgba=Image.fromarray(npimage)
PILrgba.save("result.png")

And this is the result:

Notes:

a) Your image already has an (unused) alpha channel present.

b) Any lines starting:

npimage[:,:,3] = ...

are just modifying the 4th channel, i.e. the alpha/transparency channel of the image