Sh.Rakesh Sharma Ji,
My views are as under:-
(i) It is not in dispute that you have taken voluntary registration before crossing threshold exemption limit in March, 20. Had you taken registration in the next Financial Year i.e. in April,20 it would have been better and safe with a purpose to avoid unnecessary (avoidable) litigation.
(ii) Now in case you pay GST on ₹ 2 lakhs, it is most likely (100%) that you will receive letter or show cause notice from GST department due to mismatch of figures declared in ITR and GST returns. You will have to justify the difference between both returns. First of all you will receive letter only and NOT SCN. If you justify the reasons for mismatch, SCN will not be issued.
(iii) In the case of voluntary registration (before crossing threshold exemption limiit), the registered person shall pay GST from first supply after registration. Thus that person will enter Input Tax Credit chain before crossing turnover of ₹ 40 lakhs.(we are talking of turnover of goods).