There are a few cameras, mostly early models, that altered the raw values depending on the WB. I think the Nikon D1 was one of these cases. I don't know of new cameras that do that.
Regarding getting an exact match between exposures, there are some factors that can affect this:
- exact aperture repeatability (there might be minor differences between exposures due to mechanical limitations, some brands are more affected than others)
- illumination flickering
About Rawnalyze: The histogram have a linear scale, so they are difficult to compare if there is a slight exposure difference between images. It would be easier if the scale was logarithmic (it would be analogous to f/stops) as in Guillermo Luijk's
Histogrammar. Unfortunately, Rawnalize will not be developed any further since its creator passed away and its code wasn't public.