you can get a preview of what the image will look like by unlinking the channels in the STF process (the chain link icon) and then computing a new STF for the image. the blue cast should go away.
the way to solve this is to use BackgroundNeutralization to make the background of the image grey, and then performing ColorCalibration. then if you re-link the channels in STF and recompute, the image should look (and be) right.
an alternative to BN/CC is to use PhotometricColorCalibration.
i don't think you need to do anything special with the RGB working space just to combine your masters.
rob