Right, it doesn't fill in the scratch, it does the reverse; removes clear coat surrounding the scratch and brings it all down to the same level. You wear down the the clear around the scratch to the same depth as the deepest part of the scratch, and viola, no more scratch. The change in thickness will show up on a paint thickness meter, but because it will be a much larger area with a much smoother and gradual transition from the original depth to the lesser depth, you can't see it like you can a scratch.
If the scratch goes completely through the clear coat into the base or metal, polishing won't work.