it does matter. calibration masters from an OSC should be kept in raw cfa or 3-plane/rgb raw mode. the masters will be monochrome images if in cfa format. if in 3-plane/rgb format then there will be 3 planes where each looks like a checkerboard. the black pixels in each plane are where the active pixels are in the other planes, if that makes sense.
so the darks, bias and flats should be made into calibration masters while in raw mode and kept in raw mode. the lights should be in raw mode when they are calibrated. immediately after that, you can debayer the lights and then move on to registration, integration, etc.
rob