Just found this thread and it has made for a very interesting read!
I've long had an interest in the WHL extension and various proposed terminus locations. A few years ago after reading the original idea of terminating on Loch Nevis I designed a railway route to access the Loch. Due to the hills surrounding Mallaig I chose a route that deviated from the current alignment at the village of Morar, ran along Loch Morar to Tarbet and then over the neck of Loch Nevis and onto Inverie. It would be a fairly circuitous route but would avoid the need for massive engineering other than a large bridge at Tarbet over Loch Nevis and provide access to the large natural harbour. I imagined that if it had been built then the Royal Navy would have had an interest due to its sheltered location and the WW2 commando training in the area.
Keep up the good work!