This is a nicely substantive article... but the Nate Silver article you also posted...

From Counterpunch-

The average is a 5.1% exit poll bias in Clinton’s favor

By Nate-

In 2008 the exit polls had a bias of 7% of Obama's favor.

As you said-

exit polls will attempt account for people who voted before election day in most (although not all) states by means of a random telephone sample of such voters.

and then the article continues-

this requires the polling firms to guess at the ratio of early voters to regular ones, and sometimes they do not guess correctly

Now the inconsistency between Republican exit polls and Democrat exit polls, maybe it's because the age gap/early voting gap and enthusiasm gap are much more pronounced in the Dem side, and it's harder to proportion the voter model right in the exit polls. Just my own thoughts.

The inconsistency in exit polls between states that had and didn't have early voting and had different percents of young voters, that's an interesting one. More specifically NC vs AL. Alright, here's what I think. NC had early voting and high youth vote and was on point in exit polls, while AL had no early voting, low youth vote, and was way off. What if the exit polls were off because of the opposite of what the author thought? Because the youth vote and early voting was lower and the exit polls didn't account for this? What if the exit polls were expecting a higher youth vote and underestimated how much early voting skews towards Clinton, and that's what actually caused the AL exits to be off compared to NC which was accurate? I think that could push voter difference to double digits.

The article deserves a more substantive response than what I've given thus far, but those are my thoughts at the moment.