That part says nothing about warranty at all! If you buy an MBA it will come with a small leaflet titled "MacBook Air - Important Product Information Guide". This holds the warranty on the last 3 pages (incl. the back side). It states that you have no warranty when somebody who isn't from Apple or an AASP did the upgrades and it caused damage. Since there is nobody from those two (Apple, AASP) that will do any upgrades to your MBA... There is also a part about not having warranty if there is damage when you operated it beyond Apple's guidelines.
Btw, there is no user guide that comes with the Mac any more. OS X points to the online pdf version from "About This Mac" > "More info" > "Support" > "User Manual".