The beam is recoloured by the stained glass as intended right above the beacon block (left beacon in the image), however if the stained glass is placed any higher (middle beacon), the beam is only tinted slightly, just like if the beam had gone through white stained glass beforehand (right beacon).

The comparison image shows what i assume to be the intended behaviour, where the lowest stained glass block, no matter the height, fully recolours the beam and any additional stained glass blocks add a tint.