Why aren't the main menu and the secondary menu simply regions? I noticed that you can put content pretty much anywhere ( where a theme provides regions) using blocks.

This becomes pretty straight forward and makes sense. But then I was trying to find where the "My account" and "Logout" links came from. And after some searching I found out they are configured in the Menus -> Settings admin page.

Now I read the controversy about the misleading help text for the Source for the Secondary links, so this "special" behavior to display secondary links doesn't seem to work anymore in Drupal 7.

So my question is: Why are these "regions", treated separately at all ?

Why not have normal main menu and secondary menu regions ?
So after much research I found that the main menu and secondary menu settings are there for historical reasons. They had proper functionality in Drupal 5 but its usefulness has declined over the release of newer version ( 6 and 7 ) to the point where modern themes ignore them completely in favor of the powerful regions concept.

The included themes ( as others have mentioned ) have these special "regions" still just because no one cares to remove them.

The original idea was to have an easy way to present sub menu links ( secondary menu ) dependent on the what you select in the main menu.

The modern approach is to have a pop-out sub menu ( like Superfish ) this has made the secondary menu feature obsolete.

So much so in fact, that the functionality is broken and no one fixes it.

In summary, the feature is broken and obsolete. I hope someone removes it from Drupal 8.