Can the MP-E 65 achieve a greater depth of field at the same magnification than a stopped down reversed lens?
Probably not much in the center of the frame. Where the big advantage of the purpose built macro lens would be noticeable at the same magnification compared to some reversed lenses would be out near the edges and corners of the frame. Any minor improvement the MP-E 65mm would show over your reversed EF-S 18-55mm would be due to the better center sharpness of the macro lens.
Some reversed lenses tend to soften up and demonstrate really weird geometric distortion on the edges and in the corners. Macro lenses are generally designed to provide the flattest field of focus at macro distances. Most other lenses tend to be optimized for flattest field of focus at longer focus distances. Where you tend to see the most noticeable weird effects of reversing a lens are with prime lenses that aren't that well corrected for field curvature. Based on your two examples using the reversed EF-S 18-55mm the corners are so out of focus it probably wouldn't make much difference.
The other big advantage of the MP-E 65mm is the range of magnifications, all at 1:1 or larger, that are available and the ease of use at which magnifications and aperture settings can be changed. That comes at a price, though. For each magnification there is only one useable focus distance. What we would call the MFD (minimum focus distance) at each magnification on most lenses is the OFD (only focus distance) with the MP-E 65mm. As the magnification increases the DoF decreases, just as with any other conventional lens.
Are the examples I see focus stacked?
Since we can't see those examples it is impossible for us to say.