This is the code that marked as flipped some of the bones: (https://github.com/search?q=repo%3AModdingClass%2FTK17-Custom-Bodies-plugin+isFlipped&type=code)
lowerBodyList = [ "hip_R_joint", "vagina_L_joint01", "clavicle_L_joint"]
breastFixList = ["breast_L_joint", "breast_scale_L_joint", "nipple_L_joint01", "nipple_L_jointEnd", "breast_deform01_R_joint01","breast_deform02_R_joint01", "breast_deform03_R_joint01","breast_deform01_R_jointEnd","breast_deform02_R_jointEnd","breast_deform03_R_jointEnd"]
lipsFixList = ["upper_lip_R_joint01","upper_lip_R_joint02","upper_lip_R_joint03","upper_lip_R_jointEnd", "lower_lip_R_joint01","lower_lip_R_joint02","lower_lip_R_joint03","lower_lip_R_jointEnd"]
headFixList = ["cheek_R_joint01", "cheek_R_jointEnd","ear_R_joint01", "ear_R_jointEnd", "forehead_joint01","forehead_jointEnd", "nose_joint01", "nose_joint01","nose_joint02","nose_jointEnd"]
eyeFixList =["eye_socket_R_joint", "eye_brow_R_joint01","eye_brow_R_joint02", "eye_brow_R_jointEnd", "eye_R_joint"]
specialCaseList = ["rib_R_jointEnd", "butt_R_jointEnd"]
fixList = lowerBodyList + breastFixList +lipsFixList + eyeFixList + headFixList +specialCaseList
empty["isFlipped"] = False
if name in fixList or hip_R_joint_child or vagina_L_joint01_child or clavicle_L_joint_child :
empty["isFlipped"] = True
So in practice for me the left arm joints are flipped.
So focusing on the right arm should give you proper joints orientation from start, easier to work on that first, not taking into account flipping that must be applied on the other side.