Watching my blu-ray now, and the Torfa stuff looks great. Nothing looks too dark at all, imo (it never did in the theater for me either).
I really do love that Yon-Rogg deleted scene, too. Though it would've had to be re-worked in order to be an end credits scene, because it's placement in the film was clearly before he goes to Earth (they talk of using Carol's implant - which she squashes in the climax - to track her). I'm sure it was deleted because they didn't want us to know he was already intending to kill her before he found out she knew the truth.