What was that bit about bucket fill 
quote bucket fill > mode normal, opacity 100%, fill whole selection
Still a bit of a guess as to objective but...
Is it say, the transparent area of layer#1 use to cut out the equivalent area in layer ? Try
On layer#1 make a selction Layer -> Transparency -> Alpha to Selection
Invert the selection
Down to layer: Cut the selection.
A slight difference in anti-aliasing, might be ok.
30 second example: https://i.imgur.com/K7vHT6O.mp4
quote bucket fill > mode normal, opacity 100%, fill whole selectionStill a bit of a guess as to objective but...
Is it say, the transparent area of layer#1 use to cut out the equivalent area in layer ? Try
On layer#1 make a selction Layer -> Transparency -> Alpha to Selection
Invert the selection
Down to layer: Cut the selection.
A slight difference in anti-aliasing, might be ok.
30 second example: https://i.imgur.com/K7vHT6O.mp4