Yes that is it! I want to apply the Mask layer as transparency to associated layer.
But I don't understand as to why LayersMerge and LayersMergeAll behave differently. And to top it all this difference in behavior is not documented so I am a bit confused.
Unfortunately ImageEn treats layer masks differently from regular masks. It is not well documented but I will improve this for the next release. I first want to investigate the best way to merge a layer and a mask with the developer of that code.