Light and shallow scratches can be polished out without causing visual disturbances.
But if you try to "blend" out a fairly deep scratch, you will create a small but smooth depression, or shallow "valley" which WILL cause visual distortions as you look through the canopy.
Case in point: Back in the '70s or early '80s, I was flying F-4 Phantoms in the Navy. We had new helmets that had an adjustment knob for the visor. Unfortunately, the screw that held the knob stuck out a bit, an every time we "banged" our helmets on the canopy, which was often, it left a scratch.
In their infinite wisdom, the USN decided to "buff out" the scratches. As you might have figured out, the "buffed out" canopies were MUCH WORSE than the scratched ones, because the buffer created a lens effect that literally ruined the canopies for air-to-air use. We had to order all new canopies at great expense!
Bottom line: Be very careful if you blend or buff out anything but a minor shallow scratch.