Ok, I won't defend Ubisoft or anything but we're talking about Animus here in the game. In Animus you can prepare the stage "around the past". At least we learned that from previous games.
For example I'm playing AC series from the start and right now I'm on the AC4 Black Flag. In that game there is a building in Havana and it shouldn't be in that time period (it would be finished 20-30 years later or something). In building's database entry Abstergo workers say that information themselves and they also say "Put it in game, don't worry about it".
Soooooo I think you understood where I'm coming from. Again I'm not defending any multi million company here. But with "Animus concept" they can do whatever they want to a certain degree.
PS: Hell I even remember something now
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In Revelations Ezio comes to Cappadocia by ship hahahah. Cappadocia is on the middle of Anatolia and there are no sea or rivers there. So like I said, compare to these examples some watermelon-cherry blossom overlapping seems so minor for me.