That is not the intent of section 302, rather it is a compliment of general provisions for use in application of the Florida Building code Existing Building. Your question of new fenestration installation would be governed by section 707.4 Florida Building code Existing Buildings. I would think if a new installation leaked that the AHJ would address this issue.
No, Section 302 gives guidance on use of one of the allowable 3 methods to meet the modifications to an existing building. 302.4 specifically states that like materials shall be permitted for repairs and alterations, provided no unsafe conditions is created. Water intrusion is an unsafe condition. (hazardous to the health and welfare of individuals)