Viewfinder focusing uses phase-detect AF as others have noted. The main mirror is translucent; some of the light passes through the main mirror and then reflects off the secondary mirror down to the AF sensor. There's some beam-splitting magic going on so the light arrives onto two different places of the phase-detect AF sensor for each "point", allowing the phase differences to be checked. These phase sensors are very task-specific, as they can tell not only IF focus is achieved, but if not, they know WHICH WAY TO GO to achieve focus.
Live-view focusing uses contrast detection techniques on the main imaging sensor. The selection box defines which pixels are sampled for contrast. When you request a refocus, the AF motor "runs the gamut" from <here> to full-infinity to full-macro, sampling the contrast as it goes. Once it's done a full sample, it (should) return to the point that had the most contrast. As such, it's "very easy" for the contrast-detection "action" to select almost arbitrary pixels for use as the CD region.





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