Well the reason it was chosen as his name is because Stan Lee thought it was elegant and had implied menace. Not only was he Doom, he was a mother ****ing Doctor.
As for reasons he might choose that name he has always been a man of pride and of science. There are many so called lords and emperors, and although Doom knows he is the greatest, he also knows lords and emperors fall by the wayside easily, while he would stand the test of time along with his marvelous inventions.
Also really now Doctor Victor Von Doom just has mad swagger naming potential.
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"What I'm saying is mind over matter only works when there's not much of a matter to mind. " - Lopen
The Cult of Personality.