Answered: <R1> and VEX U

<R1> states that

however, the VEX U rules allow for an unlimited number of robots

Does effectively nullify <R1>? For example, would it be permitted in VEX U to completely switch out either subsystem 1 or subsystem 2, provided that any configuration used in a match has been inspected?

Yes, supercedes <R1> for VEX U matches. So may freely switch between any number of Robots and or subsystems, provided all configurations have been inspected.