This was the point i am discussing with my friends and during my sessions of GST Audit that if the provisions of Rule 46 are not followed then penal provisions can be levied under Section 122 and Section 125. Rule 46 clearly states that on a tax invoice, the bare minimum details have to be shown and if any of the same are missing then 1st proviso of Section 122 can be enforced on the taxpayer which clearly states that penalty of Rs 10,000 per invoice. Refer to Section 122(1) (ii) talks about per invoice, so imagine if the department wants to issue notice for levy of penalty they can issue it per document which is not meeting the said provisions.
Now the same is officially clarified in the Circular #90/09/2019-GST
GST Audit report being prepared should cover this point also, so you can imagine the complexity, quantum of work involved and also the depth of knowledge required to execute it.