according to the documentation, the dcraw_emu tool should produce binary identical results to those produced by dcraw with the same command line keys. I have an example file where the behaviour between the two binaries differ. You can get the file here: https://drive.google.com/file/d/0B-kBET7UtPB9RkVzVzF6NzNWQzA/view?usp=sh....
Note that I used the following command on the file: ./dcraw -v -q 3 -4 -T ./IMG_9975.CR2
Have you encountered similar issues ? Is this a bug ? Thanks for your input :)