sychronise with kobo app

Kobo advertise with the possibility for synchronise with every possible smartphone etc
They don't tell you that's only possible with bought books from kobo
i asked them how so, there answered that the books are different formatted
i think there some extra software lines that make that the books are synchronised with the app.
So here is the question is it possible that these lines are automatically put in the file by calibre so that these books also can be read on a iphone
sorry for my bad english
Menno