I think there are a couple reasons for using studs.
The main one is that the studs line the manifold up while you fit
the big washers, etc so you don't have to worry about holding the
heavy arn thing in just the right place to line up the bolts.

Also on assembly it is normally quicker and cheaper (everything else
being equal, which it rarely is) to do a bunch of related fasteners
the same way.

Bolts and studs are usually made to different specs because the bolts
have heads and the studs don't, but you can get both bolts and studs
in a variety of strength levels, which correspond well. For most purposes,
the strength will be the same between bolts and studs in similar applications.
--
George Downs, The "original" Walrus3, Bartlesville, Oklahoma