When cars first switched to water based paints, they suffered a few teething problems too - micro rust blisters & the like. Really annoying - rust had crept right through the front wings on my 2001 merc after 5 years; thankfully replaced under warranty & the issue seems to have been overcome now. Indeed, self repairing paints are now coming to the market.
The problem BMW seem to have is the idea that they can penny-pinch on the finish yet retain a very premium price-point - centre stand, rear sub frame in particular, but engines on the GS & K16 too. Doubtless it's a risk calculated carefully, on a Worldwide scale, to account for potential warranty claims, knowing that many riders just can't be bothered to chase them down. Personally I can't get too excited about the likes of centre stands, they can have a blast/powder coat without too much stress, but the finish on the engine block is of paramount importance IMHO. The Japs do better, so BMW need to up their game pronto - this issue has been frustrating riders for far too long now & many will simply vote with their feet/wallets.