One night I woke at about 3am with a 'cunning plan' and I'm delighted to report that it actual works!
Instructions and photos follow, but I have assumed that you can already make a zippy pouch with a vinyl window.
Cut 4 rectangles the right size for the required pouch, and cut two scrap (but contrasting) smaller rectangles bigger than the required window to make the 'frame'.
Stitch the 'frame' scrap to the front of an outer piece and cut out the centre (Dont make the window too big, and I think next time I would make the outer window slightly smaller than the inner one)
Stitch an outside (framed) piece and an inside (solid) piece to one side of a zip (RST,) And repeat with the other two pieces (I used yellow for my solid lining piece so (hopefully) you can see what's happening
Outside pieces on the front of the zip and inside pieces on the back of the zip
Move your zip pull so it's about 1/4 closed, 3/4 open. MAKE SURE YOU DO THIS NOW (we shan't discuss why I think this is so important)
Cut off the excess bits of zip
Now ... get your vinyl and place it between the two window sections (with the wrong sides together) and top stitch through all three units
Stitch around the pinned areas, making sure you are only sewing through 2 layers and the other layers are out of the way
If you struggle to get access at the zip ends it might be worth stopping and flipping the unit over to see if that's easier
Turn through the opening in the lining, and stitch the lining closed
Fully lined windowed zippy pouch