A couple of points:
I agree with (1), concerning sector whiteout. It is interesting to note the despite the lack of any training, the captain was aware of the problem: At the beginning of the transcript (ie, about 30 minutes from impact), after getting the weather from McMurdo, he says "Clouds come down a bit ... May not be able to ... McMurdo. Very hard to tell the difference between the cloud and the ice."
Re (3) - I don't think it's completely accurate to say that the crew operated their flight to Antarctica in the same way as previous crews. In total, there were about 12 flights, over 3 years. They were timed to get the best weather, and they did. Of the previous flights, nearly all arrived to find perfect 'blue sky' conditions - so the crews did not pay a great deal of attention to the nav track or to the minimum safe altitude, because they didn't need to. I far as I am aware, there was only one previous flight where the McMurdo was covered in cloud, and that flight did not descend. It went to a different area.
Re (4) - I take your point about the atlas. Although the captain might have plotted the nav track on his atlas, it does not necessarily mean that he took the atlas with him - which would explain why the atlas was not found at the crash site. (But it wasn't found at the captain's house either.) If the atlas wasn't available on the flight deck, then the crew's failure to identify Beaufort Island is explained.