By default, Discourse tries to hide, for example, signatures and previous messages when you email to a category, as posts to a category are usually public. These parts are removed because they might contain email addresses the user didn’t intend to share with everyone who can read posts in that category.
I think the settings related to that are Trim incoming emails and Always show trimmed content. I remember something about Incoming email prefer HTML too. But I don’t remember exactly how they interact.
For the issue that replies create new topics disabling Find related post with key might help. But as I said, I have no experience with these settings.