Any particular religious doctrine is entirely separate from whether we have a 'soul' that can live independently of our bodies. Some scientists think near death experiences are caused by carbon dioxide build up in the brain! I wouldn't object if Trek lore definitively established the existence of the soul as distinct within the matter stream but they shy away from the religious stuff. The Barclay stuff is open to interpretation. I think he's only aware in the instant that he starts transforming from one state to another, in spite of what his perception tells his brain.