I dimly recall figuring out that the 180mm macro is more like 100mm at closest focus. Granted that's a lot longer than 65, and for all I know the 65 also shortens the effective focal length at close focus?
The MP-E 65mm is an odd animal -more like a reversed lens on a variable length extension tube. Almost impossible to compare it to a standard macro lens. Adding extension tubes to it doesn't make much of a difference in the mag (better off using a teleconverter).
Canon's 100mm macro lenses are roughly 72mm at close focus, and the EF-S 60mm is the poor man's MP-E cause it's a 37mm lens at 1x (so it only takes 37mm of extension to get to 2x, and a full set of Kenko tubes will get you close to 3x).
I bow to your experience and good results but given that you're still just 30cm/1 foot from the subject I'm surprised to hear the flash doesn't reach that far. (Not questioning you, just not what I would have expected.) (BTW I don't shoot macro with flash, rather with long exposure, so I have zero experience, just supposition.)
The problem isn't getting enough light with the flash, the problem is getting enough good light. The closer the diffuser is to the subject the softer the specular highlights. The closer the flash is to the subject the shorter the flash duration (easier to freeze motion). One of the misconceptions in macro is that the flash is always going to fire fast enough to freeze motion, and it isn't true. Motion while the flash is firing can amplify diffraction softening, an effect I call "macro motion blur", and it won't look like traditional motion blur in the image. You'll just see a loss of detail and blame diffraction for it. Even the quality and the angle of the light can impact the detail that can be captured.
You want to be able to see color and texture in the specular area, and not a white hot spot. Here's an example of my worse case lighting, cause the image was taken at 1x (at higher mags the diffuser to subject distance drops and the specular highlights get softer):
Violet Darter II by
John Kimbler, on Flickr
See how the bright areas in the dragon's eye still have color and texture in them? Same subject and light source, but now at 3x:
Violet Darter I by
John Kimbler, on Flickr
See how the bright area in the eye gets softer? There's a difference between getting enough light, and creating soft light that doesn't blow out detail. So much more than just diffraction to worry about where detail is concerned, and that's one of the reasons I don't care about diffraction.
FWIW: Both of those images are single frames (I don't focus stack) and I don't allow myself to crop in post unless I want to make a square print. Forcing myself to nail the framing with the view finder has made my composition skills better, something that the cropping tool in post can't do...