I dislike it when Obsidian does that. Because I want to be able to assign tone and intent independently from the line, which I can do in BioWare's silent protagonist games.
It's just like a (Lie) indicator. There's no reason to have that. The game should care what my character says, not what my character means by it.
I think the lie indicator is more of a sanity check for the player, especially for those who aren't fully immersed in the experience. I've been given the option to lie before having forgotten what the truth actually was. I'm not a huge fan of (lie) specifically either, because it's usually unnecessary. Either a statement is true or it's false, I don't need to be told that (unless, of course, I forget, but that's my fault).
Regardless, the presence of the lie indicator doesn't change the fact that the statement you are about to make is factually false, even if your character believes it's true. Assign whatever intent you will, but you are lying (consciously or unconsciously).