Why isn't Vy lower than the speeds for best L/D ratio and best glide ratio in an airplane with a piston engine and a variable-speed prop?
It's because climbing at Vy the engine only has to overcome the airframe drag minus the prop, on top of the thrust lift component reduction in induced drag you mentioned in your answer to another post.  

It's as if you took the prop off and towed the plane with a tow line glider style (this was done on a Wittman Tailwind back in the early 60s for some gliding drag studies to learn the plane's true L/D, with the tow line connected to the engine prop hub; the Tailwind turned out to be an extremely efficient airplane, square corners, stubby little wings and all).

Best glide has to take into account the substantial drag of the windmilling prop, so the best L/D is achieved at a lower speed.  I'm pretty sure the POH numbers are based on the worst case of the prop windmilling at flat pitch (where it goes if you are climbing at Max RPM and the engine quits), where the drag is so massive it's like you deployed a speed brake.  

You can improve this a lot by pulling the prop to Min RPM when the power is removed to try to get the governor to drive the blades to full coarse pitch. This gets you at least part way to being feathered, and helps quite a lot in the glide.