There IS another possibility. The 'Faron Zonai' could be a successor civilization taking the NAME of the Zonai while not technically BEING Zonai, biologically(or at least not FULLY Zonai). We know that the Zonai and the Hylians can inter-breed. It's the only way Zelda can have the blood of the Light Sage and the blood of the Time Sage within her. What if after the Imprisoning War a group of Hylians with Zonai blood broke away from Hyrule and founded a small kingdom in the Faron region. They could have been making repairs to the non-yeeted-into-the-sky Zonai ruins for centuries resulting into the architectural changes you see. They could have easily declined in population until the few survivors of the tribe simply assimilated into the general Hylian population. Or maybe after centuries of cultural shifts and migrations they became the Sheikah.