Application in form 10 is gateway to benefit of exemption under section 11 of the Income-tax Act, 1961. Further such form is to be filed by the due date of tax filing u/s 139.
Here is a case of an assessee in whose case the benefit under section 10(23C)(vi) stood withdrawn in 2013 and cases reopened for 5 assessment years2006-07 to 2010-11 and exemption denied. Even when the assessment/reassessments were under challenge before appellate authorities the assessee approached CIT(E) for a quick fix solution and sought condonation of delay in submission of form 10 to avail section 11 benefit on the alternative basis in  18 ITR-OL 96 (Mad). The Commissioner (Exemptions) rejected the application.
In their challenge to such rejection order the Madras High Court held that since the benefit under section 10(23C)(vi) had been denied, the benefit under section 11 could not be denied by the AO if the assessee was otherwise eligible to avail of such benefit. The purpose of assessment and reassessment was to arrive at the correct tax liability and therefore substantive benefit available to the assessee could not be denied merely on the ground that form 10 was not filed at the time of filing of the returns under section 139. Keeping this principle in mind it directed the CIT (E) to pass a speaking order uninfluenced by the reasons given in the impugned order for rejecting the application for condonation of delay in filing form 10 by extending the benefit of section 11. If the petitioner was otherwise entitled to the exemption under section 11 of the Income-tax Act, 1961, it should be extended.
In addition the Court also left an advisory for the AO that even though the Commissioner (Exemptions) had rejected the application for condonation of delay in filing form 10 by the assessee, he had to pass an independent assessment order uninfluenced by the reasons given in such order. In view of parallel remand order from ITAT, it directed AO to complete the proceedings within 3 months.