Does be isn't proper English at all. I think I can see where you're trying to go with this, that you want emphasis. I have no problem with substituting 'really' for 'do' in the first sentence.
As for #2 - "I'm afraid it's a really good dog." Is that what you intend to say? If so, then I'm puzzled. To me, the sentence makes no sense. I realize you aren't using "I'm afraid" to mean "I'm scared" (rather, you're using it in the sense of the third definition of afraid at www.dictionary.com,
which is: "Filled with regret or concern. Used especially to soften an unpleasant statement: I'm afraid you're wrong."). But if you're using it to soften a bad situation, well, what's so bad about telling someone you have a good dog? See what I mean here?
The second sentence in fact means:
"I'm afraid (you have a prejudice against all dogs), it is really a good dog!", but for terse purpose
, the content in the parentheses has been ignored. So the usage actually fits the definition, IMHO.
Talking about "does be", the "do" here is used as an auxiliary, a means of emphasis.
For example: Do be still!
(Note: "Do be still!" actually means "You do be still!")
Thus, in logic, or in some locutions(as Kara introduced), "does be " may work.
Edit: "I'm afraid (you have a prejudice against all dogs), it is really a good dog!" should be:
"I'm afraid (you have a prejudice against all dogs because
) it is really a good dog!",
The latter is one sentence.