Section 5A - Portuguese Civil code applicability

Section 5A applies to spouses governed by the Portuguese Civil Code  in Goa. Since your marriage is under the Special Marriage Act and you're a Hindu (not governed by the Portuguese Civil Code), you likely aren't eligible for benefits under Section 5A. 

Apportionment of incomes:- Since Section 5A might not apply to you based on your marriage being under the Special Marriage Act and your being a non-Goan Hindu, you generally wouldn't need to apportion incomes as per Section 5A provisions. You'll report incomes (like commercial property rent outside Goa and F&O losses) as per normal tax rules applicable to you and your wife individually in your ITRs.