I would believe the main reasoning behind this as you pointed out was to have a continuous flow as the user scans the page and allow it to blend with the design but another reason is to ensure the primary point of focus is the content of the site itself and not the navigation. There are a lot of apps which use this design to ensure the focus is on the content and the navigation is around only when you need it.
Two examples of apps which follow this layout are Angry birds and the kindle app. To quote this article about using semi transparent menu items :
Maximize the amount of screen real estate given to immersive content. In Angry Birds and the Kindle app, there are no app bars,
tab bars, nor even the space typically devoted to the iPhone device
status. This keeps the customer focused on the content and immerse in
Minimize navigation. The only navigation in Angry Birds is the "Pause" button. It's a semi-transparent button located in left top
corner, out of the way. In the Kindle app, the only navigation is the
semi-transparent overlay menu that appears when the user taps the
middle of the screen. When the user is focused on the content or
immersed in the activity, any buttons and navigation tools that do not
directly relate to the activity not only take up precious real estate,
but are also a source constant distraction. People are forced to
consciously avoid the areas of the screen devoted to controls areas
such as tabs and buttons, lest they be activated by accident. Any
effort thus spent avoiding accidentally activating unwanted navigation
detracts from the immersiveness of the activity.