Well, Barclay did say that he is being de-constructed molecule by molecule. But we know that the actual act of being de-constructed molecule by molecule is simply the process of being transformed into transferable energy for transport.
As for Barclay retaining his awareness (or sight) during transport during the energy matter transfer: Maybe we are seeing the parts where Barclay's mental awareness (or brain molecules) is in a state of where his molecules are still constructed within the transporter matter stream. Cause during the process of being de-constructed molecule by molecule (including the brain molecules) there might be no way for him to retain knowledge of the entire trip. Unless of course the consciousness mind is transformed into energy and it somehow retains it's awareness during transport while the physical body is being ripped apart and being put back together again.
Maybe his spirit body (i.e. his mental image of himself) and his mind stays in tact during transport while his physical body is de-constructed and reconstructed during the transport process.
As for Barclay retaining his awareness (or sight) during transport during the energy matter transfer: Maybe we are seeing the parts where Barclay's mental awareness (or brain molecules) is in a state of where his molecules are still constructed within the transporter matter stream. Cause during the process of being de-constructed molecule by molecule (including the brain molecules) there might be no way for him to retain knowledge of the entire trip. Unless of course the consciousness mind is transformed into energy and it somehow retains it's awareness during transport while the physical body is being ripped apart and being put back together again.
Maybe his spirit body (i.e. his mental image of himself) and his mind stays in tact during transport while his physical body is de-constructed and reconstructed during the transport process.