Unlike the Regular Moveset, the Modified Moveset has different FitMarioMotion.pac & FitMarioMotionEtc.pac files for Project M and Project+ specifically for the ThrowB_Doc animation. Project M broke how Mario's Thrown animations work which results in opponents not being properly positioned, Project+ fixed this.
It's tolerable for the regular throw animations but since the entire concept of the new animation is that Doctor Mario holds his enemy above his head, I had to animate around this issue in PM & its fix in P+.