Twitter's reply/reply-all logic is that if an @username is the first word of a tweet, it's considered to be a direct reply to only them (and thus is only shown to people following both of you). This makes sense, since a tweet that otherwise includes a username (say, "At the beach with @so-and-so!") is clearly not supposed to be a reply.

Adding a single character before the username is just a lazy way to throw off the 'first word as username = direct reply' check; using a period instead of any other symbol is more convention than a specific 'special command'.