I'm a Senior Product Designer here at Stack Exchange. I'll try and address some of your questions:
Why is the layout the same between clicking on the logo and clicking on "Questions" in the main navigation?
Well they are laid out differently, albeit not very differently. Notice the two screenshots below. The top one is if you click on the UX logo and the bottom is if you click on "Questions."
You'll notice a few changes:
- The page titles are different: Top Questions becomes All Questions.
- The "Questions" link is lightened and has an up-arrow point at it in the bottom image.
- The filter menus change.
If you're asking why we even have the two pages, think of Top Questions as a homepage. Grace Note gives a quick run-down on the differences between the two pages on Meta.SO.
Also the primary navigation seems to be changing a ton as well. Is there a better way of bringing up ever-changing options within context?
The only menuing that changes are the filter "tabs"/lines.
What it's doing now is very disorienting.
I don't disagree. I find it disorienting at times because the layouts are so similar. We can always look at making it a clearer. Thanks for the feedback!