Water seen from behind clouds now renders some faces dark with the "Improved Transparency" option enabled

This can be seen when comparing the attached images. Both water and flowing water is rendered wrong. This bug is independent of the used graphics API.

Steps to reproduce:

1. Enable Improved Transparency.

2. Place flowing water, preferably at a high elevation.

3. Fly above the clouds.

4. Look at the water.

5. ❌ Some faces of the water are rendered dark.