This could probably be a comment rather than an answer, but it surprises me that the inconsistency is status-bydesign. The How Stack Overflow redesigned the top navigation article states things like this:
We hypothesized that a lack of engagement with the nav was due to a combination of browsing habits, visual hierarchy, and the right-hand position of the layout. Based on research about F-shaped reading patterns and how readers’ eyes commonly move down the page, it made sense that our navigation was sub-optimal for most people.
And:
We also hypothesized that the focal point of the page (the logo) caused many users to skip over the small top bar. Plus the nav and top bar quickly scroll out of view when moving down the page.
But also some feedback like:
“Nav looks like tags — they might filter, but they don’t look like navigation. Makes you question what it is so I don’t click it and instead go back to Google that I’m familiar with.”
“Cleaner, more organized. Instead of jumbled stuff at top you have to read and decipher you can go to this.”
“More standardized position that you’re used to on other sites.”
“Looks really, really good. By far I like the new one — in the current one, you don’t notice the navigation at all, only the top bar. The (sub) tabs catch my eye before the current navigation.”
“In the old, it is weird to me that the two bars exist separately. This one feels more natural.”
“The new one is cleaner. Less wasted space. Things are more compact on the new one and account info is better grouped. Tabs across the top is preferable because a lot of sites have a similar flow. …much prefer the new one.”
The thing I'm trying to address is that one of the flaws of the old design, according to the article, was the shattered navigation, the questions/answers being on the right side, ... .
I'm concerned that this issue isn't being addressed with the new-new design, so I'm wondering how you think the new-new design tackles this issue.