Talia - The differentiation between the two is not mine or even FanPro's, and no one is saying it is desirable now. In fact it no longer exists per se.
It was a concious (and necessary IMHO) decision made by the developers at FASA when SR3 was released not to force new players and old to buy 10+ books (ie. the White Wolf route) for the rules if those could be compressed and updated in 6/7 books at the cost of the fiction/fluff component. They chose to cut down the number of core rulebooks and the result is SR Companion, Magic in the Shadows, Man&Machine, Cannon Companion, Matrix and Rigger 3 (Revised or otherwise).
The need for this separation was no longer there even before FASA closed and it hasn't been since. Under FanPro the book formats include both rules and fiction elements although they are kept separate (such as SOTA's alternating fiction/rules setup or T:AL's or SSG's rules additions in a single Game Info section at the end) and that's the way it looks like they'll stay for the forseeable future.