Auto-align and layer masks

Hello Everyone,

I am trying to get a definitive answer if Auto-Align layers takes into account masks that are applied to the layers you are auto-aligning.

Two scenarios, both involving a stack of layers. Each layer contains a different exposure of the same photograph.

Scenario 1: The photos in the layers are a bit misaligned. You notice this problem, determine a layer to use as a reference image. You create a mask and mask out the parts of the photo on this reference layer that are in motion between the exposures, like trees swaying in the wind or clouds moving, etc. You lock this layer to make it a reference layer for auto-align and run auto-align.

Question: Will the auto-align ignore the areas of your reference layer that have been masked out?

Scenario 2: You didn't notice the misalignment and started blending the layers using masks. Eventually you figure out you need to run auto-align, but now most of your stack of layers have masks attached.

Question: Do you disable the masks, but keep the masks linked to each layer, then run auto-align? Will the masks take on the same geometric distortions as the layer they are linked to, as auto-align does it's thing?

Any help would be appreciated. A few tests I've run produce inconclusive results.

Thanks!