Hi Rob,
Thank you for telling me about the master flat. It is useful to know.
It is true that we almost always need to re-adjust the color of a calibrated/stacked image. This is why I had never paid attention to the color of flat. I only noticed this issue recently, when I need to further stack two groups of stacked images taken in different years. Because my flat changes, the two stacked images have dramatically different colors. The very different brightness of each of the RGB layers from different years means that when they are stacked, they will be given artificially wrong weighting. I don't quite like this. Of course, there are ways to work around this problem. But if the flat has a neutral color, then this problem will be gone.
Another reason to preserve the original WB is for non-deep-sky photos, as you pointed out. Last month, I used PI to calibrate my images of solar corona. However, because the flat is not white, there is a color shift after the images are calibrated. I ended up with using Photoshop's raw conversion to restore the WB of my PI-calibrated images. It will be much nicer if the PI-calibrated image can have the right color right out of the box. I am not sure re-normalizing the RGB brightness in the flat can solve this though.
Cheers,
Wei-Hao