A bit late to this party and more about BIMP limitations rather than Gimp / GEGL
BIMP does have some strange characteristics, for example, png's will always have an alpha channel even when flattened. BIMP has a list of reserved terms, which is why some entries are absent from the pdb. Selections are ignored, all sorts of things.
This driving me crazy, tried some things over the last couple of days without success.
I use the split python for GEGL, a little script for the commands and gegl_command.py to do the work.
The attached is a mix of GEGL / gmic / Gimp layer mode. Nothing special, a test.
Attachment:
bimp.jpg [ 141.56 KiB | Viewed 5382 times ]
Starting with a transparent layer (1) and I can get an effect (need to refresh the layers) (2) or export to a jpeg (3) result as expected...however...if I use BIMP, rendering to a png is ok, same as (2) Using jpeg all the hidden pixels in the alpha channel are exposed (4)
Just a comment that BIMP is a great tool but has 'quirks'
![Wink ;)](./images/smilies/icon_wink.gif)