I would hope that this hidden meaning would not apply all the time where a blessing is concerned. I would be curious how many southerners agree with this as a generalization.
Ask around... you’ll find that it is a very common Southern practice to substitute “bless your heart” for a more vulgar insult.
When it is spoken about a baby (for instance, one that has just got a 'boo-boo' or some such thing), then it can be taken literally. Of course, the vocal inflection in such cases makes it easy to understand.
When it's sarcastic, you know it.