In my view, interest is to be paid on net tax liability. This interpretation holds good even in absence of proviso. This is because of following two main views:
1. Section 50(1) uses the word "tax" as against "output tax". Had the intention of law is to charge interest on gross tax liability, the expression could have been so used.
2. Section 39 requires an assessee to file return by due date. It nowhere says that return is to be filed after payment of taxes in full. This can further be corroborated with the meaning of "valid return" given under section 2. As per circular 07/07/2017-GST, department has acknowledged that return can be filed without or with lower payment of taxes. But the said functionality was not active on GST portal. As a result, if assessee was not able to knock off his gross tax liability to the extent of input tax credit due to system restrictions, he should not be penalised by way of interest.
Also, doing so interest has been made in penalised nature whereas it is always compensatory in nature.