This way it doesn't come off an an accusation, it keeps the conversation going, and is generally much more constructive. I found that people who "call out" logical fallacies and the like are generally looking to "win the argument" rather than actually have a conversation.
Calling people out on "bad faith" is common; there's an entire string of terms for this ("gaslighting", "sealioning", "concern trolling", what-have-you). I've never seen it end well. If someone is actually engaging in bad faith then it's better to disengage and call it a day, and if someone is engaging in good faith then all you've did is insult them without actually contributing all that much.
I haven't heard the other two terms, and wouldn't be able to guess what they mean.
Sea lions spend all day fighting over [arbitrary thing] to impress potential mates. I'm certain this happens on social media, and that most potential mates are as impressed as they are by an actual sea lion. :-)
Concern trolling seems to be too specific a term.
IMO it's an annoying corruption of what was actually a rather useful term, but there you go.
Engaging in a good-faith argument, especially with those you often agree with, yes. "Calling out" - I'd be hesitant about that.