should be parallel to the body in a recessed floyd rose body.
the neck pocket being angled allows the neck to be angled, which in turn allows the floyd to be setup with the posts higher off the body, then allowing the tremelo to be setup parallel to the neck, which in turn allows some floating trem action on a guitar that has no recessed cavity. this allows flutter's and small floating action on non-recessed guitars. again, this is only the case if you dont have a recessed cavity.
if you have a floating tremelo and a fully recessed guitar body, it should be setup properly parallel to the body.
if you setup the floyd flush with the body on a non-recessed guitar with the neck pocket being cut at an angle, there will be small intonation issues and/or fret buzz problems.