The problem is that they feel the need to include that at all. Other characters start out badass, Lara needs a sexual assault to become one. This has been explicitly mentioned as the developers as what starts her development. Why, why the hell does this need to be the case. Why all male characters have gender neutral origins but female characters need one that constantly reminds us she's a weak female.
And you see, even if all these problems were there, and what we saw was Lara beating it all, this wouldn't necessarily be a bad thing. But so far every single interview makes it clear the point is to have her suffer, to show her as weakling, wounded, cornered, all promotional material is about just how much she can get hurt in a 3 minute demo. You can't make the game a soft torture porn, have her be ok at the end, then say "Wow, how empowering!" This is not a game about "Lara is in such a fucking shitty situation, but look! She can beat all of this!", it's about "Lara is in such a fucking shitty situation, let's see how she breaks her leg now. Now the arm. Now I dunno, fire on the face". Perhaps the game DOES end up being like that. But promotional material and the comments from the developers are not selling this image.
You can't seriously be arguing they want to empower Lara when this game is as targeted to the male crowd as pretty much every other big game, and when they are telling us is to protect her. She's not powerful. She needs the gamer's protection.