Body bag or coffin; I don't think either would haver been involved in bringing down this aircraft. I have flown both and they are easy to secure so that they don't move and Air Frontier has had enough experience in transporting deceased to ensure it was done properly.
What is not clear is whether there were two persons and the deceased on board or only the pilot and deceased. I suspect the latter as it would be very difficult to get a coffin into a C210 and keep the R/H front seat.
Should weather be the culprit in this crash then the flight routing should be looked at. I found during my time in the top end that the afternoon cells liked to play out along the points of land and that by going offshore you could more easily get around them. However, there can be a real danger in getting under the cloud shelf of an approaching cell. The turbulence can be mind-boggling even though you are not in cloud and can be a trap for young players.
Whatever the cause, I hope the ATSB does a proper investigation as there will be lessons to be learnt for the other young aviators struggling to gain hours who are the likely candidates for this sort of charter. My condolences to the family of the pilot who will now be struggling to understand how their son could come to such a sudden death.