В случае, если кому-то нужен ответ здесь:
oiiotool A.exr --ch R B.exr --ch B --chappend A.exr --ch G --chappend --chnames R,G,B -o mix.exr
Чтобы разбить, что это значит,
* read A, take just its R channel
* read B, take just its G channel
* Append channels of the the top two images, yielding A.r,B.g on the top of the stack
* read A again, take just its B channel
* Append the channels of the top two images, now you have A.r,B.g,A.b
* Force new channel names R,G,B just in case they carry their old names or got confused
* Output to mix.exr