I really, really doubt that this apparent rape scene will make it into the finished product -- but if it does, it'll surely be a terrible covering of the topic. It's like comic books, in which any time they want to give a female character a troubled past they wheel out the old rape theme. It is never a male character, and that's going to be true in videogames for the foreseeable future as well.
UH male characters get raped in comic books all the time, as part of their character development.
Berserk: Main character raped as a child by racist caricature, learned how to use a huge sword to fight off much bigger rapists. I'm serious about this. This was a big part of the plot. Someone back me up, here.
Spider Man: Peter Parker raped by his uncle, which gave him spider-powers (his uncle was a spider). This was the original story, they retconned it later. Not many people know this.
Indiana Jones and the Temple of Doom: The cultists raped him in the comic book version. They dwelled on this scene for two whole issues. The second issue was the same as the first, but with new art covering different angles.
Superman: Origin story involved him being raped by a golem that loved to commit crimes (the golem was also made of kryptonite).
Batman: Raped by his parents, the guy that killed his parents, and at one point a swarm of bats.
My point is it's NOT just female characters that are raped or threatened with rape to make their stories adult and mature and grim and dark and exciting. There's nothing strange or creepy about the Tomb Raider reboot at all. It's definitely not using sexual assault as titillation for what they assume is a primarily male audience. An audience that wants to feel like they're protecting the defenseless, battered, shivering Lara, while also getting a half-boner.
Also Phubans what the hell prompted you to try to discuss this here?