not sure if I buy the idea of Samantha basically being a female version of her brother.

I didn't read it so much as being a female version of him. I assume he's the one who's been taken in this scenario, and so she's become the one working the X-Files because of the impact the abduction had on her. I always thought "spending lots of time trying to learn about UFOs" was a pretty reasonable life choice for someone who believed they'd seen a family member abducted by aliens.

It's logical that they'd have other things in common (channel surfing, smirking :); they're siblings.