The roof and quilt box help to minimise heat loss through the top of the hive / make the thermal dynamics of the hive more similar to a hollow tree (where the trunk above the hollow would provide insulation).
The space in the hive can be increased by nadiring (i.e. adding new boxes under existing boxes as the existing boxes fill). This means less empty space in the hive, making it more thermally efficient (and thus simpler for the bees to control temperature / more likely to survive the more extreme temperatures).
The honey provides an insulating layer which aids the hive's temperature regulation.
Outside of equatorial regions, the brood naturally moves upwards into the honey supply during winter feeding. Thus having the honey above the brood avoids bees not finding their honey supply and starving during winter.
Instead of purchasing one, it's fairly simple to build your own at a fraction of the cost. Instructions are freely available online:
http://warre.biobees.com/plans.htm
https://thebeespace.net/2008/07/30/introduction-warre-beehive-construction-guide/
Honey bees evolved over millions of years living in hollows in trees; by hollowing out a log you're creating an environment very similar to their natural habitat and thus most likely to fit with the bees' needs (i.e. including any we may not yet be aware of).
If you're keeping bees for honey, rather than simply to keep bees / aid their regeneration, this hive is not for you; the hive is designed solely for bees to live in; so no facility is given to allow honey to be simply extracted.
Because of the complexity of the hive it cannot be self-built by most people, and can only bought from a single manufacturer; thus allowing them to charge a premium for this product.
This means you can only get liquid honey; not honeycomb. Also, it is also believed by many that the natural wax is superior to plastic for a number of reasons:
Plastic causes "off-gassing"; i.e. the release of airborne particulates / chemicals, dubbed volatile organic compounds, which may be harmful to the health of the hive.
The cell size is fixed. Cell size relates to the sex of the bees produces, so this restricts the bees ability to alter their drone:worker populations.
Bees communicate by vibration; natural (wax) comb will vibrate as expected, whilst plastic will not.
Wax can store pheromone information which may be important (though as yet there is no science to support or discount this claim).
http://www.honeycolony.com/article/3-reasons-to-go-against-the-flow-hive/
https://attheapiary.wordpress.com/2015/06/22/the-flow-hive-solves-a-problem-that-doesnt-exist-exacerbates-a-problem-that-does/