Summarizing.
1. For your customer you are nominated supplier of pass-through parts.
2. Your total quality performance score is affected by concerns related to pass-through parts.
3. You manage (lead) corrective action process for pass-through parts concerns.
Did I understand it correctly?
I guess scope of your automotive QMS covers pass through parts too.
If parts are made in Japan, then IATF requirements apply to them too.
Problem is, first you have not identified manufacturing among remote supporting function you get form your HQ.
Second, they are not IATF 16949 certified.
Third, most important, they resits, and that's nothing new for me, as I know their approach very well.
You are in bad position as long your customer reports concerns, monitor performance including pass-through parts.
If it is not reported, so auditor won't mind otherwise he is obliged to audit your interfaces with HQ.
And it won't be nice for you and your HQ too.
Two options.
1. Discuss matter with your customer and exclude pass-through parts from your performance and satisfaction score.
2. Discuss with HQ their approach to development of their QMS towards IATF 16949 certification.
Probably you won't succeed, so prepare for mayor nonconformity during future 3rd part audit for 4.3.1 and then you won't be able to do too much within <90 days.
Last option
3. Try transfer Japan production to you or local supplier.