I think the difference is more boring than that.

I agree that the 2006 and 2019 seasons are very similar from a myopic Notre Dame fan's perspective. I don't mean "myopic" disparagingly, I just mean that they're similar if you're just comparing those 2 ND teams in a vacuum without any consideration towards other teams' results, ND's preseason ranking, or the timing of ND's losses.

In 2006 ND started the season ranked #2.
In 2019 ND started the season ranked #9.

In 2006 ND dropped 10 spots to #12 after their first loss.
In 2019 ND dropped 3 spots from #7 to #10 after the close loss to UGA.

In 2006 ND rose from #12 to #6 before their 2nd loss through sheer attrition during their 8 straight wins over unranked teams.
In 2019 ND rose from #10 to #8 after 3 straight home wins including ranked UVA and unranked but talented USC.

In 2006 ND dropped 6 spots to #12 after their 2nd loss.
In 2019 ND dropped 8 spots to #16 after their 2nd loss.

In 2006 ND finished #11 prior to the bowl game.
In 2019 ND will probably finish #14 if Oregon loses to Utah.

The big boring difference between 2006 and 2019 is that every team's ranking is affected by the results of other teams competing for the same rankings. By the time they lost to USC in 2006, there just weren't enough good teams left to pass them up. They did get passed up by every 2 loss team from the Big 12, SEC, and Big 10 just as they did this year (except for Minnesota who is behind us), and they remained ahead of VA Tech, WV, Wake Forest, and Rutgers. Hypothetically, if this year Michigan beat PSU, Bama beat Auburn, and Baylor lost any one of the several close games they played, we'd probably luck into a #11 ranking just like the 2006 team did. And similarly some other teams' results could have left the 2006 Irish ranked lower than #12. It has nothing to do with equity in my opinion, it has more to do with attrition by other teams, or lack thereof.

More evidence that we don't have any more or less equity with pollsters is that the 2006 Michigan loss dropped ND 10 spots while the 2019 Michigan loss dropped them "only" 8 spots. These drops have more to do with how early/late in the season it happens and what other teams' records are.