Thinks are clearer with a screenshot of your Layers list...
If you initialize by transferring the alpha, the layers original alpha is made fully opaque, so the final result depends strictly on the mask. If you use other options, the final alpha is a combination of the layers original alpha and the mask (more or less applying the mask in "Darken only" mode to the original alpha).
If you want a layer to be limited by the contents of another, the classic solution is to to "Alpha to selection" on the layer with the shape, and on the other layer, add a layer mask, and initialize to selection.
In Gimp 2.10, a better solution is to put the two layers in a group, and have the "Composite Mode" of the top layer set to "Clip to backdrop":
Attachment:
ClipToBackDrop.png [ 212.17 KiB | Viewed 650 times ]