You don't want the nut to "reach the bottom of the threads" (commonly called being "threadbound") because in the case of the Focus wheel bearings the nut would not be applying any clampup force which is what is required here. The torque applied (including what the torque wrench was indicating) would be meaningless. The torque value range specified is required to have the nut apply the desired clampup force.
As to the OPs original question......the torque values/torque procedures listed in the Owner's Manual, the Service/Shop Manuals, TBs or Tech Tips have not just been pulled out of thin air. The listed torque values such as in this application are determined by engineers who take the expected loads, the materials used, fits and clearances etc, into account. In the example of the rear wheel bearing/axle nut, obviously if you got really carried away and went way over the specified torque you could shear off the end of the spindle, or you could over stress it and you wouldn't know it until it broke off when you were driving along.