Retarget definatley is a huge step backwards from the great .fbx merging tools 9.6 had.
I get the feeling that MAXON employees don’t really use, or understand Motion Builder.
I don’t think the retarget tag can handle a single parent type hierarchy.
The kind of parent->child heirarchy a typical IK rig with controllers uses.
You have to use separate joint chains for it to work:
LeftArmRootNull->LeftUpArmJoint ->LeftArmJoint->LeftHandJoint
RightArmRootNull->RightUpArmJoint ->RightArmJoint->RightHandJoint
SpineRootNull->hips->SpineJoint->Spine1Joint->Spine2Joint->NeckJoint->HeadJoint
LeftLegRootNull->LeftUpLegJoint->LeftLegJoint->LeftFootJoint->LeftToeBaseJoint
RightLegRootNull->RightUpLegJoint->RightLegJoint->RightFootJoint->RightToeBaseJoint
Export from C4D as .fbx and characterize in MB.
Then plot and export an .fbx animation with from MB. And merge it into the above rig.
C4D puts the animated bones from MB inside each joint chain.
Then place a retarget tag on each of the C4D joint chain root nulls.
The source will be the top most bone merged into each joint chain from MB.
The target will be the root null in that particular joint chain.
It works. But it’s not pretty.
It definately needs to be updated.

Hope this is helpful.