Minimum Interior Door Height
The Code Does not stipulate the height of doors in bathrooms. Yes, you are correct that the Code does indicate that ONE  3'-0" wide x 6'-8" high door is required for "habitable spaces". However, only living, sleeping, eating and cooking spaces are defined as "habitable spaces". "Bathrooms, toilet rooms, closets, storage rooms, utility rooms, halls and similar areas are not considered habitable spaces." (R 202 of Code)

By the way, the Code does stipulate the ceiling height of 7' for, "habitable rooms, hallways, corridors, bathrooms, laundry rooms and portions of basements containing these spaces." Now, there are four exceptions for sloped ceilings, beams that hang down below 7', etc. (R 305.1).