Whether ITC reversal is applicable on sale of Mutual fund units under GST?
Answer: Yes, in view of Section 17 (3) read with Section 2 (101) of the CGST Act, 2017 read with Explanation 2(b) of Chapter V of the CGST Rules, 2017
If yes, then under which GSTIN is the reversal to be made if a taxpayer has a PAN India presence?
Answer: Wherever there is common ITC involved (i.e. goods / services - on which ITC is availed and which is used for transaction in securities) inviting Rule 42 & 43
Additionally, whether such reversal is required to be made even from a SEZ GSTIN?
Answer: Yes, only if there is common ITC involved (i.e. goods / services - on which ITC is availed and which is used for transaction in securities) inviting Rule 42 & 43.
Lastly, lot of industries - specially bigger one having multiple GST registrations all over India - are grappling with these questions as raised by you. One needs to properly structure entire business operations to minimise the damage or controversies arising out of those questions.
These issues can be specially troubling for tax-payers trying to get benefit out of second proviso to Rule 28 of the CGST Rules, 2017 for service-supplies between distinct persons as specified in sub-section (4) and (5) of section 25 (For example: HO / corporate related services (generally known in Market as 'Cross-charge))
So, it is suggested to take comprehensive review of existing tax-compliances of any organisation as a whole and take suitable structuring thereto (wherever needed) of business operations to minimise the damage or controversies arising out of those questions. One can always seek help & assistance from Expert if felt needed in this.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.