Sure, but that's not really an answer.
I think most people would say that the likely answer is no. Nathan Drake is a powerful character because of his strength and his depth. Showing a male rape scene would by perception make him lose much of his power with the way our culture is socialized to think about male rape.
In the case of Lara Croft it seems that this is more about exploiting the fact that she's a female character and it's "ok" for them to face being raped.
If it played out like Lara's video (he kicks the shit out of the gay and shoots him in the face, after his advance), even if Drake didn't killed the guy, it would work.
I can't list from the top my head but I do remember a few Villain-Hero sexual tension (and cues to "rape") in movies, even if unwarranted by the hero.
If anything I believe that an actual attempt of rape in Uncharted, if Nathan Drake as the victim, it would be played out with humor. Maybe as an attempt to make that villain tension work, or just a crazed thug that felt he had the time to humiliate/enjoy Drake.
A serious tone rape (or attempt), as seen on American History X and other movies, would be assumedly more complicated. Generally, sad or not, male to male rape is taken lightly. So how to fit it in the narrative style from Uncharted (if not a reread)? This emotional trauma would have what type of leverage to the character or influence in his journey? I honestly can't think in a worthy construction right now, but will try.
Lara's event is actually (exploitative or not) well placed. Rape is a common occurance in those situations. Having her kill her first person and deciding she cannot weaken at challenges (as she doesn't in the video of that scene) is not actually a character building event, but a character demonstration one. Her friend is still kidnapped, this alone sets fear and determination, because again, they could kill/torture/rape her friend. They are not being willingly fictious there. The necessity or choice can be questioned and/or objected. But it is not far-fetched or "played out" as many try to paint it.
Again, we have to wait and see. The concerns may prove real when you actually play the game, and the event ends up feeling loose to the rest of the narrative.
But no one knows, assuming things based on the backpedalling is naive at best.