Even with the A3 Hatchback vs Sportsback, the wheelbase (and therefore back seat space) is still the same. The extra 8 cm is added behind the rear wheels. So you have more luggage space, but no more seated space.
With the most cars, the 3 door model has longer front doors, moving the B Pillar back. So as well as the better looking exterior, some people like 3 door models better (such as myself) for the fact the B pillar is behind your perpherial vision. The 5 door Golf is particularly annoying to me on that front. In my family we've got both a 5 door Golf and Focus diesel and the Focus's back doors are smaller in comparison to the Golf's back doors, so the B pillar position isn't as annoying on the Focus as the Golf. But then, many people have always driven 5 door cars and so this just doesn't bother them.
On the current Polo model, a good friend who is something like 6'5" wanted a Polo 77TSI, but couldn't get in and out of the 5 door model cause the front doors are so short and he just couldn't get into the seat easily. No such issue with the 3 door Polo GTI, but the 77TSI isn't available in 3 door and he didn't want to spend as much as a GTI.
So it comes down to more than just looks... but there is never a difference in back seat space.
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