Ideally, if one is willing to take risks & face rigors of litigation etc. but interested to availing ITC in such a situation, same should never have been paid subject liability under RCM through Form DRC-03 with interest & penalty.
Given situation is not covered u/s 74 as ITC was available against subject tax liability under RCM & period involved was very initial stage of GST implementation in India. Hence, no penalty u/s 74 should have been paid.
One can also argue that due date of paying taxes under GST for period from July, 17 to Mar, 19 is still not lapsed and hence, interest u/s 50 (1) is also not payable.
Lastly, importantly, one should have paid subject liability under RCM - without any interest & penalty - through regular Form GSTR-3B by raising self-invoice u/s 31 now and then, take ITC against such invoice so generated now.
As said before, these line of action are for those who are willing to take risks & face rigors of litigation etc. but interested to availing ITC in such a situation
Obviously, one can never be certain about how legal jurisprudence will evolve in various issues connected with above arguments (including about time restrictions u/s 39 (9)) and only time will tell.
But now, taking ITC in given situation (where taxes are already paid under RCM with interest & penalty through Form DRC-03, based on audit objection from Dept) looks more difficult & risky.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.