I think that's your answer, right there. She has a very old-fashioned view of gender roles, and for a man to cook or clean must mean there's something 'feminine' (and not in a good way) about him, thus the comment about CDing. She may have meant it as a joke or as a veiled/low-level insult (that's for you to decide), but it probably doesn't mean that you've been outed. If she knew you were a CD, you'd probably hear her opinion loud and clear. I suppose you could always try opening conversation by mentioning a news article or TV show on trans/CD people* and see what her reaction is.
* The remake of Rocky Horror with Laverne Cox is coming out in October, though that may not be the best way to introduce the topic. I've heard good things about the show Transparent but haven't seen it myself.
It would be a shock, but I personally wouldn't have a problem with it. I can see how a lot of people might, though.