I saw this the first time in Rawtherapee, just used IrfanView to take a screen shot.
Thanks for the tips guys!
It looks to me like Raw Therapee uses the active area as well. I thought it had an option, but I don't see it. However, you could easily make a profile that starts with the crop set to the normal image area.
If you use a flat field, that can significantly reduce the border effect.
Note that the presence or size of the dark border may depend on the zoom level.
In the CHDK code, my preference is for the active area to include everything that contains recognizable image data, because you can salvage the darker parts in a pinch, and most programs don't make pixels outside the active area accessible at all without editing the exif.