A suggestion: Add "Mask" mode for layer compositing. "Mask" mode would
affect the alpha layer of resulting image. Full white in the current layer
would multiply image's alpha by 1.0 (identity function), and full black or
alpha=0 would multiply the image's alpha by 0. Gray values would make
portions of the image transparent.

This functionality would be similar to "Layer Mask", except that a layer
mask applies to only one layer. A "mask" layer would apply to all layers
below it in the stack.

Currently, the layer modes do not affect the alpha channel of the resulting
image: the new alpha is always an additive combination of the current layer
and the one below. "Mask" mode would add similar flexibility in
manipulating the alpha layer as exists for manipulating the images, value,
RGB, or HSV.

Work around:
Define a layer mask and apply to all layers that require masking. Changing
the mask is a pain, however.