Which would have lowest drag?
 

I'm wondering which aero modification would be the most beneficial for this hatchback. And no, boat tail is not an option as all vehicle modifications are forbidden in my country and it has to look OEM :)

On the left is a base model with no aero.

In the middle small trailing edge extension is added as can be seen on almost all modern production vehicles nowadays.

On the right spoiler is added with small gurney flap on the top to make angle between top of the roof and top of the spoiler as shallow as possible.
This design was quite frequently used in the 80's (Kadett GSI, Audi 100 wagon, Car and Driver Pinto) and is proven to work but nobody uses it anymore.

Is it because trailing edge extensions are better at lowering drag, or is it in fact superior solution and manufacturers abandoned it only because it might not look "cool" enough for today's car buyers?

First off a tuft test is needed to see if there is separation on the back window without mods. if there is separation pic 2 with the mod at the top would be best. if partial separation towards the lower part of the window the 3rd pic would be best.

Ya don't need a tuft test on that one!

All the same. If anything, the small roof spoiler #2 may make like .3% difference, essentially insignificant. Keep in mind that air is being significantly affected out to 1 meter, so a 10cm add on will do little to change the gross air flow. People have a misconception that only the air within a few centimeters of the car is important and such is not the case.

Picture #3 would do nothing, guaranteed. If you want to make a significant change, you would really need to make a large extension on your car like this which you say is not possible.

Modern cars have been significantly improved in their roof shapes, particularly where the top of the front windscreen meets the roof, this radius has gotten considerably larger, as well the roof shapes in general are much more curved on hatch backs, by doing this it eliminates the need for a spoiler.

On some cars, the angle of the rear hatch and how the transition was made really created a huge lift, for these a 10cm spoiler was a significant change by not allowing the air to try and attach at all.

The angle break on the car illustrated is too much for the air to remain attached, so the spoiler will not help much.

I say only the roof spoiler would do anything. Might want to look into why, how and variants.

http://ecomodder.com/forum/showthrea...tml#post404651

whats the angle of the rear glass. if it is near 30°, which is a very bad angle to be, then I would go for the top spoiler to provide a clean cutoff for the air coming off the rood.

I don't know what else you have done to the car, but grill blocks, belly pans, an air dam. would all be invisible and help. So would removing the mud flaps

Skoda
 

From drag tables published by Hucho,the Soda's rear slope may be so steep as to create a squareback type wake,which includes the entire rear face of the car.
To get to a 'fastback' wake,the upper tip of your lower spoiler would have to create a roof-to-spoiler angle of about 25-degrees.Even with this,you'd be creating vortex drag.And your separation line remains essentially the same,so your base pressure of the wake would be constant.
Just to begin with,you'd need to extend the roof out as Kamm recommended,and this is illegal.
A complete side photograph of the car would be helpful.
There's about 7-criteria involved in deciding an 'optimum' rear slope.The more information the better.