Bear in mind that vorticity cannot be converted to pressure recovery.Without the gentle transition into the down/in-slope,you'd always have a drag penalty from the VGs.If the flow didn't reattach,the entire wake would take on the pressure of the point of first separation.
And they'd have to be tailored precisely to match the boundary layer thickness where they were attached.
If only the trailing edges of your mini tail touched the 'Template,'you'd have reattachment without VGs,along with captured-vortices,of which the inviscid flow would skim across.
The low pressure of the vorticity would be sequestered away from the wake,allowing for pressure recovery and a higher base pressure,lower pressure drag.
Without blowing,or suction.there's only so much VGs can do.
I think your plan WOULD reduce drag,compared to doing nothing.It would make for a fine project,and so far as I know,your combination has never been attempted.
Look at the back of the Mitsubishi Lancer,and the trailing edge of the trunk,compared to the roof height.This should guide your mini tail architecture.
