For alpha 0x01, I've been able to trace this to an issue with cairo.
Using python-cairo:
a 0xff ff ff 00 background is incorrectly mapped to a 0,0,0,0 pixel.
a 0xff ff ff 01 background is correctly mapped to a ff,ff,ff,01 pixel.
Note that somehow, inkscape makes it worse by incorrectly handling alpha 01 .. 09 as well.
I will file an issue with cairo, but please leave this bug open, as I think the alpha issue in inkscape exceeds this.
For alpha 0x01, I've been able to trace this to an issue with cairo.
Using python-cairo:
a 0xff ff ff 00 background is incorrectly mapped to a 0,0,0,0 pixel.
a 0xff ff ff 01 background is correctly mapped to a ff,ff,ff,01 pixel.
Note that somehow, inkscape makes it worse by incorrectly handling alpha 01 .. 09 as well.
I will file an issue with cairo, but please leave this bug open, as I think the alpha issue in inkscape exceeds this.