In or out of context, "I don’t care if they target a government agency I don’t like"means the exact same thing. It’s a stand alone statement not impacted by your second sentence. That’s just not true. The fact that it can form a complete sentence on its own doesn’t divorce its meaning from the surrounding context. In my favourite example, “I want to make sure the children die with the parent” is a complete sentence, but outside of a programming context, it’s quite fucked up. In this case, the sentence you quoted is equivalent to a parenthetical to add nuance to the second half you omitted: “They’re just another bunch of assholes out to make a profit (even if they target a government agency I don’t like).” It’s the opposite of a standalone statement: It’s the subordinate qualification to a different, standalone statement. Just because you can quote it outside its context doesn’t mean that it’s independent of context.