Hi, yep I have fitted several sets of windows now for builders. As JD says there is nothing wrong with the plexi, it is the fact it is a pillarless door that causes the problem when combined with the plexi which in its nature is slightly flexible.
Other issues are that the pug (as with most 'new' cars these days) learns the window position & relies on a force feedback to set its upper and lower positions. With it being pillarless it also drops a cm or so when the door latch is operated so it clears the rubbers. All this can be a bit tricky to set up with the new runner positions etc. I have lost count of the number of hours I have spent with my arms inside these damned doors working blind! Oh & make sure you have someone within earshot when you do, as if the car suddenly senses too much pressure when you are adjusting it does the safety 'full window drop' which will trap both your arms & have your fingers if they are in the scissor part of the mech. Can you guess how I know this!
The angle of the window is also greater to allow for the lower roof, so the bottom of the window needs to push out to where the side impact bar was in the door.
As JD said, they will flex if opened a few cm at motorway speeds, not a lot, but enough so they dont seat back into the top when closed if still at speed. You just need to wait till you slow to close them unfortunately. Its not an issue & no adjustment will change them, its just something you have to live with when you have plexi side windows.
Main advice i would give is not to treat the side windows as a last job, make sure you get them done early before the outer skin of your door is bonded, that gives you the best chance to get them right & the best access possible. Also get the door handles and latches done and working at the same time, as with the window in the right place the levers etc are very close to the window.
Sorry I havent done any of the A3 windows, JD is your man for those!