Just in an attempt to better understand this.....300.3(B) states that conductors in different cables
shall comply with 300.20(B). In your example, this can not comply. And since your example cannot comply, then 300.3(B)(3) does not pertain.
As I see it, 300.20(B) is intended for like phases to be installed in PVC conduit for ease in termination, and due to hysterisis when entering metal enclosures a groove must be cut to minimze such effects whereas if all of the conductors of the circuit are contained within the same conduit this is not a problem.