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The reason Vref is 4.096 is because the designer wants full-scale to be 4.096. It could be 2.5 or 1.25 or 3.3959395.
Without showing us the rest of the schematic there's no way to know what the function of that zero ohm is, but my GUESS is that it gives you the option of using the 5V supply as Vref if you leave the regulator out.
You are confusing the digital thresholds with the analog input resolution. Vref determines the full-scale (all 1's output) value for the A/D input. You do know what an A/D does, don't you?
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