There is no mention of any kind of limitation clause for the eligible applicant anywhere in the Gratuity Act. I don't know who introduced this 90-day rule, and everyone is repeating "90 days, 90 days" everywhere.
Limitation is only applicable to the employer, and they are subject to a penalty in the form of interest as well as fines in case of a delay. If, after 90 days, you are not eligible to even apply for gratuity, why does the act state that the employer has to pay interest at the rate of 10% per annum for the delay from the day the applicant becomes eligible for gratuity?