Worth saying that what I've had done to my ID.3 isn't technically much more invasive than just replacing the front speakers. You will be plugging 2 wires (right and left audio channel) into third party equipment - the front speakers. My installer has also plugged 2 wires (right and left audio channel) into third party equipment - the amp and powered sub. In terms of repurposing the factory wiring, the only thing extra in my setup is that the installer will have had to find a switched power source from somewhere.
Of course, my install will be more detectable by a dealer than yours. But if VW denied a warranty claim for something big that isn't related to either the audio, or panel rattles where my installer had the door cards off etc. and I took them to court, it would be interesting to see them argue how the problem could have been caused by tapping into two audio channels and switched power! Though I suspect unless it was something ruinously expensive out of warranty, I wouldn't go to the hassle of taking them to court and would just glumly pay up.
But, bottom line, in terms of wiring what you're proposing isn't much less invasive than what I had done. If I've put my warranty at risk (whether I've put it marginally at risk, or significantly at risk is a matter of forum debate!), you will be putting your warranty at some theoretical risk by replacing speakers too.