well... i think we're into terminology confusion now. a "stack" is the same as an integrated image. in other words the terms "stacking" and "integration" are sometimes used interchangeably to mean "summing images to increase the final SNR". "master" is also used to refer to an integrated image ("master dark" - an integration of a bunch of dark subexposures, "master light" - an integration of a bunch of light subs).
i think you are referring to ChannelCombination - the process of 'merging' 3 or more monochrome images into an RGB image.
so yeah, sometimes you will do some processing to each channel's master image before the combination. you might do noise reduction, or deconvolution, or match levels between the channel masters with LinearFit before creating the RGB image. but generally speaking there are only 3-5 master images depending on what you are doing, so the need for batch processing is not really there (and also you probably need to apply different NR parameters to each filter's master light, or different deconvolution settings, etc.)
rob