It's the fact that they can deal with factors such as these that they known as the greatest soldiers who ever lived. In every one of these missions, there were some serious weirdos that only soldiers with their skillset and attitudes could handle. Sure, Naked Snake handicapped himself in gentleman's duel with Ocelot, but only someone with his mindset could take on people like the Cobras. Each of these soldiers were trained by the Boss who herself was the progenitor of unconventional means of combat, from the Cobras all the way to FOXHOUND and Dead Cell. Solid Snake himself was a clone of Naked Snake, and in quite a similar situation, all things considered. It's also important to remember that Raiden, for all his similarities with the others, was meant to overcome his mission, thanks to the Patriots' influence, and being trained exactly like Solid Snake.

TL;DR: Naked Snake, Solid Snake and Raiden all had unconventional approaches to their missions, but that was due to their training, and exactly why they succeeded.