It is nowhere specifically mentioned that section 50(1) or section 50(3) will be applicable on availing ineligible ITC. But then you have to admit the fact that the GST Law is poorly drafted.It is a total omission. The method of calculation of interest as per section 50(2) is itself not prescribed in the rules and further as per various court judgments where the method of calculation is not prescribed if required under law then there can be no levy of tax or. interest as the case maybe.
Now coming to our point the reason I am suggesting 18% is that if you notice the flow of the law all the rules mentioning reversal of credits states that amount shall be added to output tax liability or it is clearly mentioned that interest under Section 50(1) will be applicable. Even for section 42 & 43 it written that amount of reversal shall be added to output tax liability in GSTR-3. But the act here is clear that interest shall be charged @ 24% therefore 18% in this case is not applicable. Since reversal of ITC becomes part of output tax interest of 18% should be applicable
Also take the present case that after availing ineligible ITC the taxpayer has paid his taxes so in effect he hasn't paid his taxes. So here it is another reason that 18% is chargeable.
A view can also be taken that no interest can be charged in case where ineligible ITC has been availed but not used as there is no specific provision. As per recent High Court Judgement that in case of interest also adjudication has to be done where interest has been challenged by the taxpayer. In that case under which section or rule will the officer adjudicate interest.
So there can be various reasons for various interpretations. But as per me 18% is correct as it takes into account both the essence and the intention of the law.