I always believed that 90 day reporting is a totally separate issue from anything to with extensions; IOs, particularly in rural areas, will often do a 90 day report simultaneously....... absolutely no help if you are already reporting online.
I see no difference between an extension date on a visa or on an extension. If the visa is 'live' then 90 day reporting does not apply (except O-A's) - you have to leave the country every 90 days.