Simply load and bin one stack at a time (in mono) and save each one unstretched. Then, once you have them all binned, composite them as usual in the Compose module.
Not to confuse you further, but if you wanted, you can you can composite R, G and B, then bin that composite, and then save this composite unstretched. This way you get 3 channels in one file. When compositing the binned LRGB, simply load the composited file 3x times; once for R, once for G, once for B. L will have to be its own binned file (TIFF obviously does not deal with LRGB, but just RGB).
Hope that helps!