The cam_ext.cfg included with SS2Tool crops intro.avi, which is NOT letterboxed. That's because you're excluding the Thief cutscenes from cropping instead of the SS2 cutscenes.

That is, this:
; (thief) list of movies to exclude from cropping (only used if "crop_movies" is enabled)
movie_crop_exclude credits.avi+success.avi+death.avi
; (shock) list of movies to exclude from cropping (only used if "crop_movies" is enabled)
;movie_crop_exclude intro.avi+credits.avi

instead of this:
; (thief) list of movies to exclude from cropping (only used if "crop_movies" is enabled)
;movie_crop_exclude credits.avi+success.avi+death.avi
; (shock) list of movies to exclude from cropping (only used if "crop_movies" is enabled)
movie_crop_exclude intro.avi+credits.avi