[arnarbi]

Stained glass won’t (I think) shift any frequencies. It will attenuate different frequencies differently, but it won’t make up new ones.

So when the signal frequency changes, you’ll still see that change, but the light might get brighter or dimmer at the same time due to the stained glass. But you don’t care about the brightness to begin with.

[carlmr]

In the stained glass case, maybe you need to go digital where brightness and color don't matter, but only on-off state.

[ploynog]

You'd be surprised by the amount of brightness and color produced if you are turning things on-off sufficiently fast.

[ykonstant]

Related: lots of optical illusions.