They're only spawned when someone researches Archaeology, and never on GPTI.
If you see embassy on sites, it's placed after they spawned but before the owner had Archaeology (or they simply prefer placing embassies on resources?). Those can never be excavated since embassies are permanent.
If you see embassy on sites, it's placed after they spawned but before the owner had Archaeology (or they simply prefer placing embassies on resources?). Those can never be excavated since embassies are permanent.