Even if we err on the cautious side and say a better comparison is replacing just the transmission of an ICE vehicle, the Tesla drivetrain is only electrical connections (albeit some large ones), drive shaft, and mounting hardware.
I wrote out the list of ICE transmission removal steps but deleted it -- I think the point is clear: this is no big deal.
Tesla can absolutely reuse the drivetrains it removes, unless the defect is catastrophic. I wonder what exactly the cause is? (I'm sure Tesla is hard at work determining just that.)
Just speculating: if Tesla has gone ahead and extended the warranty, they might be doing it because they are certain that the issues are not catastrophic. Cost/benefit analysis was probably completed to Musk's satisfaction before this announcement.