Major form factor change? They squared up the case and enlarged the screen by a MM. That's it. The only major change is *rumored* to be the health sensor, which may or may not include a blood pressure sensor. That is a part though, whos design would have been finalized months ago and should have been in production well before now.
As for actual assembly, again that process has not changed: Machine the outer casing (now square externally but internally mostly identical other than being physically larger by less than 3%) attach buttons and crown mechanism, drop in sensor, then battery and attached SoC then screen, apply heat and pressure to seal the entire assembly. Test for functionality and then box and pack.
If they are having QA issues then that is most likely on new assemblers, not a design change, something that wouldn't have come up until actual assembly began in earnest. Think of it like a new hire: they might have aced the interview but it isn't until they're on the job that problems become clear.