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I added up all of the state vote margins for Trump and Clinton from the 2016 election and subtracted any part of the margin that was over 51% of the state vote total. I attributed any votes beyond 51% of the total as wasted.
Using this definition Clinton received 1.1 million wasted votes due to geographic inefficiencies (vote margins concentrated in states she already won). This accounted for 0.85% of her popular vote percent.
If you consider any votes beyond 50.5% of a state's total to be wasted, then Clinton wasted slightly more at 0.86% of the national vote.
Most of the disparity between the polls and the popular vote can be attributed to shy Trump voters.
Given the geographic disadvantage and the shy Trump voter effect I would deduct 2% from any margin a Democrat may have in polling.