FWWM Laura sees who
I would think that too, except for that very last scene of Bob/Leland talking to Laura in the train car after he shows her he has her diary pages. He comes in from the right as Leland and says "I always thought you knew it was me," and then comes in from the left as Bob and says, "I never thought you knew it was me."
So with that in mind I'm thinking she always sees Bob's face, but because she continued to question him so strongly about who he really was she might have broken through her own ability to see? Maybe? Does that even make sense if Bob thought she was always seeing Leland (since she was 12??) that he would tear the pages that reveal that secret out of her diary? I guess it was the only written evidence.
As I recall we only hear "I thought you knew it was me," So I suspect you're referring to a deleted scene which is not part of the official movie.
Who can see Bob's true face: "the gifted...and the damned." We know Laura is damned, so she saw Bob. Maddie is damned so she sees Bob once he decides to go after her.
Fire Walk With Me