i found a page which has all the informations about assassins creed and i've been entering it for long time but today it came to my mind to read about Aya "Amunet" and see if it was mentioned about her tomb being in Italy in AC2 and in egypt in Origins.
and here it is, read the below. we finally know lol
Quoting from the assassins creed wiki
By the time of the Renaissance, Amunet was respected as a great Assassin, and a statue of her had been placed in the Assassin Sanctuary of Monteriggioni.
Though buried in Egypt, alongside her husband, a shrine dedicated to Amunet was located in the Basilica di San Marco in Venice, Italy. The Assassin Ezio Auditore explored the shrine and took the seal from the sarcophagus, which helped him to acquire the armor of the Assassin Altaïr Ibn-La'Ahad.
In 2017, her sarcophagus, along with her hidden blade, was found in Egypt by Layla Hassan, who cut out a genetic sample from the mummy and hooked it up to her portable Animus to relive her memories".
so i think this is the official story about having a tomb in italy and then in egypt they found one.
the link to the Assassins creed wiki below