When I add www.example.it/de/ to my GWT sites, it don't ask about verification (because the main domain was already verificated**).**
In Setting/Geo Target there is:
Destinazione geografica Il dominio del tuo sito è già associato alla destinazione: Italia
Translated: Geo target the domain is already associated to target: Italy
the same is for the root domain.
Geo target is only for generic domains (and some other particular domain)
bye