The argument is, to take Boston and Miami as examples, whether or not point differential justifies ranking a 6-4 team over an 8-2 team, particularly when the 8-2 team has already beaten the 6-4 team twice. To me, when you rank the 6-4 team over the 8-2 team in that situation, it demonstrates there's something profoundly wrong with your evaluation.
In a subjective ranking made by people, I think you're right. There is no reason that two Boston wins head to head over Miami shouldn't have them higher. (When combined with Boston's otherwise stellar record)
But adding head to head conditions to an automated power ranking wouldn't make it more accurate. Fundamentally head to head match ups are a small sample size and the raw scores don't tell the story. Not to mention you're ranking a ton of teams so head to head factors would create a nightmare for a regression. It wouldn't increase the predictive power of the model. (Cavs swept the season series with the Spurs in 2006-2007 for example)
The system doesn't consider match up factors, injuries, and a whole host of other subjective factors. (for example back to backs or the last game in a 4 in 5 days sequence)