Finally got the time to check this out.
Simple fix. In Object Mode, Select the Armature, then Press “Match Reference”. this solves the rotations for the Legs. You may have issues with the toes after:
to solve the toes; simply combine the Toe_Ends with the ToeBase. (_end is reserved by Blender, and shouldnt be used as is anyway)
I forgot I had moved the bone orientation fix from Fix Scale and Rotations (this only does general rotations of mesh and armature) to its own button.