It shouldn't matter as long as you are consistent.
Print the image negative in the same manner as the ChartThrobe negative (greyscale, RGB or CMYK) with the same printer parameters.
It's been a while since I did it myself, but I guess you can simply input the raw scan in RGB to get the correction curve. If you desaturate first so R=G=B but still in RGB mode, that should work too (not sure I understand why it wouldn't, after all that is just like a very neutral print.) Perhaps there are some subtle differences in the exact correction curves arrived at the two different ways, but I would think the basic tonal relationships shouldn't be too far apart. So the ultimate digital negative would be fine.
:Niranjan.