The Rad2Refl is only a conversion. It stays at TOA. That’s why it is not an AC. It is explained in the help.
You can find the quality_flags already in the L1 product. If flagged as invalid the Reflectance is not computed. You can enable an option, than it is copied into the resulting product.
You can check the flags with the PixelInfo View.
I checked your product.
In your case the NaN values result from TOA radiances which are zero.
I consider this as an issue and create ticket for it. (SIIITBX-185)
Thanks for the report