A reply here is not a comment. It's a thought of its own: it makes a point, and anyone can answer it.
What that changes
In a comment section your reply sinks. Here it stands on its own: it can be answered, upvoted, or argued with directly, and it carries your name into every conversation it touches. What earns a reply is not the fastest thought or the loudest one. It is the one that gives someone something to answer.
Say the thing, then say why
The reason is the reply. "Agreed" and "this is wrong" are both verdicts, and a verdict gives the other person nothing to answer. One sentence of why turns it into a conversation.
Answer the actual point
Pick the specific sentence you are responding to and respond to that. It is the difference between a thread that goes somewhere and two people restating themselves.
You don't have to pick a side
"I don't follow the step from here to there" is one of the most useful things you can post. So is "you have changed my mind about this part, not that part."
Disagreeing well
Go at the position as hard as you like. That is the whole point of the place. Going at the person is what gets moderated. The test is simple: are you making the argument harder to hold, or attacking the person making it?
Read the guide: Replying with a thought