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Ambient exposure is indeed tied to the focus point (actually, an larger area than the normal 5º spot, as I mentioned, because metering automatically switches from Spot to Evaluative when you go from ambient exposure to ETTL).
Because I'm focusing on a face, which in the case of my mostly-Caucasian clients is brighter than a gray card, I set the flash exposure to overexpose slightly to compensate. The ambient meter setting determines the contrast ratio between the flash and the 'fill', which is the ambient light. The lower the ambient setting, the darker the area not exposed by the flash, i.e., the shadow side of the face, the background, etc. I like to set it to about -1/3 to -2/3 stop to give the flash just enough pop to light the face properly (and also allows me to standardize my WB to the Flash setting on the camera) without giving an artificially 'flash' look.
Questions #2 and #3: No to both. No need, because the above method works just fine.
#4: The only reason ETTL would underexpose a full body shot is that the flash is too far away or that the aperture was too small to give the proper exposure to the subject. I've never had this issue, although even with my groups I shoot at f/8. You could test this by racking up the ISO in a series of identical tests on the same subject (same settings throughout). If your exposures start getting better at the higher ISOs, the flash isn't powerful enough. If nothing happens, you've got something else going on. But the use of any kind of light modifier should not change the exposure (of course, it WILL require more light in a modifier, but ETTL should compensate).