According to the RPGs also made by Fantasy Flight the stormtrooper corps is still separate from the Imperial army as in the Legends background. 'The common citizen of the galaxy will never see an Imperial Star Destroyer or stormtrooper' according to Age of Rebellion core book.
While stormtroopers are seen in the movies, it's potentially because the movies are dealing with key areas. If Vader wants something done, he's going to use the best after all.
I figure it's kind of like the Roman Empire. Legionaries were comparatively rare compared to the auxiliaries who made up the majority of the military forces. That said, legionaries would be present at most major battles and were deployed to defend the most important areas, becoming 'the face' of the empire even two millennia on.
