PR updated with new logic. In brief, "WB RGGB Levels Measured" will be used if there is an indication that it preserves the dual-ISO behavior (50D), otherwise "Raw Measured RGGB" is used (everything else so far). Which tag is used is printed in the cr2hdr output (right near the end), as well as a warning message about a possibly out-of-date exiftool if it can't find these tags. So, here's where we stand:
Marsu42's files (6D):
IMG_8666.CR2 5900 +8 (normal)
DUAL8668.CR2 4150 +25 (Raw Measured RGGB)
DUAL8669.CR2 4400 +27 (Raw Measured RGGB)
--
default 5600 +20
Audionut's files (5D3):
_46A9808.CR2 4350 +48 (normal)
_46A9809.CR2 4400 +28 (Raw Measured RGGB)
--
default 5500 +19
My files (50D):
IMG_0689.CR2 5450 +13 (ISO 100)
DUAL0688.CR2 5700 -4 (ISO 100/800, exposed for 800)
--
IMG_0709.CR2 4800 +27 (ISO 400)
DUAL0708.CR2 4750 +27 (ISO 400/100, exposed for 400)
--
IMG_0707.CR2 4400 +21 (ISO 400)
DUAL0706.CR2 3900 +19 (ISO 400/100, exposed for 400)
--
IMG_0715.CR2 4850 +30 (ISO 400)
IMG_0717.CR2 4800 +28 (ISO 100, exposed for 400)
DUAL0714.CR2 4650 +26 (ISO 400/100, exposed for 400)
DUAL0716.CR2 4500 +26 (ISO 100/400, exposed for 400)
--
IMG_0718.CR2 4300 +23 (ISO 100)
DUAL0719.CR2 4000 +3 (ISO 200/100, exposed for 100)
DUAL0720.CR2 3500 +10 (ISO 400/100, exposed for 100)
DUAL0721.CR2 3400 -24 (ISO 800/100, exposed for 100)
DUAL0722.CR2 3900 *** (ISO 1600/100, exposed for 100)
IMG_0723.CR2 4250 +24 (ISO 100)
--
default 4850 +46
Just with these shots, this fix seems to work decently on everything but the 6D, but there needs to be more testing across a variety of lighting conditions.