In nearly every other interface within MediaWiki the controls for interacting with content is above the actual content. That's not the case in Flow.
Examples of other interfaces:
* Navigation menu (Username, Talk, Preferences, Watchlist, etc)
* Tabs for Read, Edit, View History
* Wikitext editor
* Nearly (all?) Special: pages (RecentChanges, Contributions, etc.)
Other bits of the MediaWiki universe that have their controls at the bottom:
* Echo - In the drop-down sheet "All notifications" and "Preferences" are at the bottom, but that's for another task :)
Akin to designing applications that are specific to an operating system, there are best practices to make the application feel congruent with the use of other applications on the same platform. In this context Flow's bottom toolbar feels out of place.