does the metal water piping under counters and @ water closets need to be bonded when a nonmetallic water piping (Pex) is used throughout the remainder of the building
No, isolated sections of copper pipe that aren't likely to be energized, don't constitute a "Metal piping system" and therefore are not required to be bonded.
See 250.104. I know it is not code, but the commentary
in the handbook under 250.104(1)(A) drove this point
home for me, based on a sensible judgment call.