Can't all be wrong
I have very few flower macros that aren't stacked, but here is one as an example. I shot this at f/10, rather than the slightly smaller aperture I would usually have used, because I wanted to keep the background out of focus. I took this with a tripod and focused manually with live view, if I remember right. You can see that a lot of it is sharp as a tack, but even at f/10, the depth of field is not enough for the whole flower.
Re diffraction: I wouldn't worry about it unless you close down a lot, for two reasons. First, the effects at apertures like f13, even on a crop, are minor. Second, unless you are going to print large, the increase in DOF is likely to more than offset the diffraction in terms of the overall impression of sharpness. As an example, I usually use this photo, which I took with a Rebel XTi and a 60mm macro when I was first starting on macro. It looks quite sharp, and there is an 8 x 10 (A4) hanging on someone's wall. I shot it at f/20.
Dan