I explain the differences between the two flags (mostly) in an answer from when they were first separated into two. That should help with the "which to use" part of your question...
As to the flagging practices... I'll preface this by saying that I've seen the flag you're talking about. I'm not really sure I agree with it, even after seeing your explanation here. It's about advertisements conditioning viewers... which is... not completely untrue. Regardless, this isn't about your specific flag so...
Comment flags are special, so keep that in mind. For the time being (and hopefully not for much longer) moderators can not (without a user script) decline a comment flag and delete the comment in one click. Because of the UI, they have to do them as two separate steps, in the right order, and may need to open the post the comment is on in a second tab. This means it's much more likely that a moderator will decline a comment flag and not remove the comment - particularly in cases where they feel the chosen flag is too harsh.
Even still, our moderators are quite diligent and do regularly delete comments that are flagged with the wrong reason if they still believe that removing the comment is appropriate. Note that it's much rarer on meta sites for comments to be removed than on main sites. Meta is designed more for discussion, so comments tend to be the standard method for that.
You ask whether there's a penalty for the harassment flags that doesn't come with unfriendly flags - there is not. They are, for the time being, treated the same by the system. They trigger auto-flags at the same rate. There is no penalty for no longer needed flags or custom moderator flags.
So, what should you do if you feel that a comment flag was dismissed wrongly - use a custom flag. Particularly in cases where it's a single word that's problematic, pointing that out for the moderators' attention will help them do their jobs better - they may have just missed the troubling word or they may be so used to seeing that word that they don't take it seriously. Explain why you think the comment should be removed.
There's another option - one that I generally hesitate to recommend because it can be somewhat uncomfortable in comments - but if it's a single word and the rest of the comment is otherwise valuable, suggest that the word be changed (edited) - and even recommend an alternative word so that they don't have to stumble for the right choice.
So, you could in your example say
I think the word "brainwashed" here is rude to people from {country}, could you change it to "conditioned"? That should retain the meaning but not be so unkind.
The flag may still be declined but if you convince them by being specific, they may agree... and if you get it declined again, you can either move on, knowing you tried, or... if you really feel that strongly, make a meta post about it on that child meta site - not here on MSE.