My impression is that the post 107 launch chimneys were adjusted in angle so as to allow a bit more of a laminar flow down around the top sides of the side pods. With them in the more vertical position it would seem to me that they would have behaved more as endplates with regards to the flow over top of the sidepods, which considering their angle of attack might well have given some lift, which would have to be counteracted somehwere giving a net drag penalty.
as i see it.