I disagree with it being confusing but I do agree with there being an option to change it back simply because some admin's prefer to have the customer visit the site to see the content than have it in the email!
I'm confused. Don't we already have complete control over what's in the email notifications via the phrases? (phrases like watched_thread_reply_email_html) I was assuming that the variables that are available might have expanded with 1.1 but we still have full control over what is in them. (with the phrases getting "mail merged" via the settings in the "Email Templates" under the development tab, if exposed)