How should the number of maintenance hours per flight hour for the C-17 be interpreted?
I am sure the raw data can be found somewhere in some document or budget line item but there are a few things to keep in mind. 


These numbers may only be airframe maintenance preformed. According to this article it seems that P&amp;W maintains the engines. 
This article (a bit dated) states that the air force must only maintain 50% of the work in house. Again they may only be counting their hours. 
The air force (and all military aircraft) are subject to their own regulations and intervals and such. Although they must play by FAA rules when flying in airspace their upkeep is to the standards set forth by the owning military body. This may make it hard to compare with general aviation or commercial aviation.  



  Do the required maintenance hours scale with: size, complexity, military/commercial use?


In general yes. A piper cub is going to be simpler to maintain per hour than say an F-16 but as you know things vary. I would say that the hours scale more with complexity than size. Mainly because from a mechanical stand point a more complex engine or aircraft would have more things to disassemble and go wrong and in turn more things to put back together generally increasing maintenance time. Keep in mind this is a very general statement. 

In terms of military vs commercial use, you will see a lot more maintenance on a military fighter than a commercial plane largely as a result of design. Commercial planes have lots of redundant systems and reliable parts as they are selling safety. Fighters have lots of high performance parts, some redundancy and things that may be made to wear faster in order to preform. Again a general statement but you can get the gist. 


  Do those 20 hours refer to an average over extended operation of the aircraft? In other words, does this include extended maintenance where the plane might be undergoing days of intensive maintenance, skewing the numbers?


Im going to assume that this is an overall average but it may not be.