I can't see the Audi S3 (or any other A3) being put together any better than an R (or any other Golf) either. It just won't happen if you understand high volume and lean manufacturing techniques employed by car manufacturers. Robust work instructions strictly adhered to (which will be common to all the mainstream VAG models) for those jobs with a human input, common tooling/templating, and standardised robotics on standardised and validated progreamming for the automated stuff etc. Time is money, every job will have a tolerable limit on it and a fixed window of time to do it if there is a level of adjustment rather than "one way only" guides ("peg in hole and secure around" type lining up of components) - they don't have time for fettling 1/10th of a mm here or there before the next car is coming through. If anything is fixed beyond tolerance then it will be flagged for readjustment later if it does not impede further build at that point.
To get the kind of perfection that is imagined Audi achieve, you need to look at the likes of the glass factory in Dresden where the Phaeton is hand-built by technicians wearing white cotton gloves.
Under the skin, almost all of the parts are the same, is there a better way of screwing the Audi together than the VW (or Seat or Skoda) when almost all of the parts are the same? Reliability surveys show that Audi does not sit at the top of the VAG tree, it is distinctly average on that score, along with most of the rest of the VAG range.
Exterior-wise, the A3/S3 is every bit as likely to suffer the same degree of orange peel (which is not at all bad by today's standards with the use of water based paints - BMWs and Hondas are much worse), the body panels are welded in the same way. Everything working off the same platform (MQB for the latest Golf/A3 and others) will be built the same way.
We've seen the Seat Exeo take over where the last gen of Audi A4 left off in the same plant as it was essentially the same car with a Seat interior and a rebadge. Did they move the Audi people on and bring in Seat people trained to a lower standard and see building standards suddenly drop off when the Seat model took over and the new A4 went elsewhere?
When you buy any mainstream VAG car, you get standardised building techniques throughout. When you buy an Audi over a VW then you get plusher door cards, part/full leather seats as standard....and a serious lack of standard equipment.