When you look at clouds through stained glass blocks or panes they are still white.

Interesting. Seems that there's an issue with the rendering order of clouds/transparent textures when you are the same height or above the clouds (very similar to particles/transparent textures, see MC-9553). Doesn't happen when you're underside the clouds because the bottom of clouds is not transparent (MC-997).
Attached a screenshot showing clouds seen through ice and stained glass (from above).

EDIT:
I would change the title of the ticket to "Transparent textures render behind clouds" and mention in the description that this doesn't happen underside the clouds because of MC-997

OK, seems to be a dublicate of MC-34658. Someone please change the title of MC-34658 to something like "Transparent textures render behind clouds" (it's not easy to find with the current title) and mention in the description that this bug doesn't happen underside the clouds because of MC-997.

After some generalization, dublicate of MC-9553