Due to the way that the MP-E is constructed, basically a reversed lens on a variable length extension tube, I doubt we'll ever see an AF version of it.
If you can learn how to control were the depth of field is going to fall in a scene then focus stacking, for the most part, isn't necessary. I took this shot in the heat of the day and although I didn't get close every time I tried I only need to get close once.
Tech Specs: Canon 80D (F11, 1/250, ISO 200) + a Canon MP-E 65mm macro lens (set to roughly 2.5x) + a diffused MT-26EX-RT (E-TTL metering, -2/3 FEC). This is a single, uncropped, frame taken hand held. In post I used Denoise AI, and Clarity in that order.
Violet Darter VII by
John Kimbler, on Flickr