"If it's alien, it's ours."

It's worth remembering that the big sinister organization wasn't actually competent at much besides being scary, looking good in suits, and nearly destroying the world. (Parallels to Ianto in Cyberwoman are deliberate.) The big scary organization is gone. It died at the Battle of Canary Wharf. This is the tale of what survived.

Think about Torchwood's mandate for a moment. Their job is to handle dangerous things that no one understands. They get paid to play with fire, and to be the ones who get burned instead of the general public. To take away all the insanely dangerous alien shit and hide it away where it can't hurt people, and then hide the evidence of it where the evidence can't scare people.

Their business is to handle alien things they don't understand. If those things weren't alien, if they were understood, they wouldn't belong to Torchwood. "If it's alien, it's ours." If it's not alien, if it's familiar, it's not ours. If people could understand it, it wouldn't be our responsibility.

And since they're always handling things they don't understand, they never quite look as competent as the people who get paid to handle things those people do understand. And since they are what survived the Battle of Canary Wharf, physically (Ianto) or ideologically (Jack), they're honest enough not to pretend an understanding they lack by the very definiton fo their job.