Whilst VAG own VW, Skoda, SEAT and Audi I have a feeling they not only all have a degree of independence when it comes to styling, but they also have their own profit and loss to look after.
If VW make more money on a Golf vs Skoda on an Octavia, I guess that is down to how they compete within the group.
If they all had to take the same line then their wouldn't be any point in them existing as competing products.
The commonality is to do with major component design, the styling is entirely down to the marque. Its easy to see a A3 as a Golf, but its not and cannot be because otherwise you simply wouldn't bother trying to market them seperately, they would just be trim levels and even then you wouldn't bother because having 35 trim levels would increase cost and confuse the consumer too much.
Therefore they have to be distinctly different.