The Kobo fb is indeed setup in BGR order, not RGB.
Code:
red: bitfield offset: 16, bitfield length: 8, MSB is right: no
green: bitfield offset: 8, bitfield length: 8, MSB is right: no
blue: bitfield offset: 0, bitfield length: 8, MSB is right: no
alpha: bitfield offset: 24, bitfield length: 8, MSB is right: no
Pixel format details:
B: 0 / G: 1 / R: 2 / A: 3 (i.e., BGRA)
Should alpha be honored? Yes.
This is *mostly* harmless since the display is ultimately grayscale, but it does minimally affect the grayscaling process, as red usually isn't weighted the same as blue, no matter how you choose to grayscale.
The point is entirely moot (outside of in-book content) once you've setup Calibre to handle the grayscaling on its own for covers thumbnails

.