The intention for this feature is to make it easier for your readers to comment on your blog. My dad fits into this category. Instead of having to visit my website, he now can simply reply to an email notification of a new blog post or comment.
I can appreciate that as I have several readers who I know outside of the blogging world and in the past they've replied via the post's emails, but of course the emails went into limbo somewhere. :)
Today, I tested again using Gmail (a non wordpress account) and replied leaving in the quoted text. It went through, requiring modification. And it was cleaned up, showing only my actual comment. That's good... but I do have a concern about my readers' privacy. The username I have for my Gmail account is pretty generic, so that's fine. But what about those who may use their full name , not realizing their user name may post on the blog.
If any of my email subscribers reply, is the best action to just edit their name as needed? I've done it in the past when one of the readers signed in with their Facebook account, not knowing their full name would be used in the comment.