I understand both the bride and groom need to be present for the actual marriage ceremony under the Special Marriage Act. But is it also required for both of them to be there when they file the application 30 days beforehand?

No, both the bride and groom are not required to be present when filing the application under the Special Marriage Act. Only one of them needs to be present with the application and necessary documents. However, both must be present during the marriage ceremony itself.