the 'uncoupled channel' autoSTF is very useful for seeing what your data 'really' looks like.
if you are happy with it, i suppose you can just transfer the autoSTF settings to the HistogramTransformation tool, thus stretching your image. this is done by dragging the STF triangle to the strip at the bottom of the HT tool (where the HT tool's triangle, etc. live, but don't drag onto those icons or it won't work), and then applying the HT to your image.
having said that, here are a couple of caveats:
1) one usually needs to run DBE on the stacked image, since invariably there are always gradients. if you have run DBE with 'normalize' unchecked (default), it will have the effect of roughly aligning the channels.
2) probably ColorCalibration should be used to fix your color balance after DBE. I think one should run BackgroundNeutralization before running CC.
3) there are a lot of ways to stretch an image (AdaptiveStretch process, MaskedStretch script, HistogramTransformation). you may not want to use HT to do the initial stretch in favor of MaskedStretch.
the processes in point #2 require careful tuning of the high/low pixel value parameters to make sure you are only picking up the pixels you are interested in. if you want to spatially constrain the pixels the processes are looking at, define previews in the areas you are interested in, but then use the Region of Interest setting and take the coordinates from the preview ("from preview"). if you save a process icon for CC, this will make it portable to another image without having to remember where to create previews and update the process to point to the new image's previews. this is useful if you add integration time to an image and you want to re-do all your processing.
