Definitely go with the trousers. Shorts are going to be call back to the overly sexualized previous incarnation. Besides, going with a pair of rugged, reinforced pants would go a way to showing that Lara has learned lessons from her experiences on Yamatai. She's prepared to get down and dirty, whether that be working a dig or fighting for survival.
The 'Survivor' tattoo ... I don't think it's really necessary. Want to hint at the previous game? have some of the scars she got still around, maybe faint. Or have her carry both of Roth's pistols in the 'classic' hip holsters. There's many ways to go about referring to the previous game in her character design without something as blatant as a tattoo.