The SS Appam was in fact captured by the SMS Mowe, a merchant raider of the Imperial German Navy.
The Mowe was disguised as a neutral cargo steamer, so that it could get close to targets. Not only was this vessel successful as a 'commercial raider', but sank a number of merchant vessels during WWI.
The Appam was then redirected to Hampton Roads, Tidewater, Virginia, US, in effect bringing a prize of war into a neutral port. The British and African Steam Navigation company, filed a suit to recover her from the Germans. Federal Judge, Edmund Waddill of Virginia, in a 15 000 word opinion, directed, 29 July 1916, that the Appam, with the cargo (valued at between 3 and 4 million dollars) remaining on board and the proceeds of the perishable cargo already sold, should be restored at once to her British owners (wikipedia).
Of the many theories surrounding the disappearance of the Waratah, I am surprised that a similar scenario to that of the Appam, is not included.
If it is to be believed the Waratah was conveying a significant quantity of gold in her bullion hold, this could be considered a prime motive to 'highjack' the steamer.
The Waratah had sufficient coal to take her across the Atlantic to some obscure South American port. It seems very unlikely that a team of 'highjackers' would have boarded the Waratah after she departed company with the Clan MacIntyre. Mutiny would be a far more feasible option.
Personally, I do not believe the Waratah was subjected to a forced take-over or mutiny. But if whirlpools and methane gas were postulated, why not add this one to the list.