See video. Here's the explanation.
If I apply a layer mask and then bring back the mask from transparency (Layer -> Layer Mask -> From Transparency) the color of the layer is unaffected.
If I have this mask on a group and Merge Visible (Layer -> Merge Visible) and then bring back the mask from transparency, all pixels that were black on the layer mask will now be white.
These pixels should not be turned white, they should retain their color as they do if you apply the layer mask.