According to that logic, since Two Sicillies doesn't exist in 4.000 BC when you'll start your game in Ancient Era, shouldn't you automatically loose?
In my humble opinion, premise of Civilization game isn't the same as Europa Universalis. You'll play as immortal leader of one of the civilization that begin their journey right in the beginning of the men. Your civilization doesn't become Two Sicilies, it is one right from the start.
When you'll start in Ancient Era, you'll do that as Two Siclies, not Sicinians or Etruscans. When you'll start in Classic Era, you'll do that as Two Sicilies, not Rome. When you'll start in Medieval Era, you'll do that as Two Sicilies, not Arabs, Normans or Kingdom of Sicily.
Look at some vanilla civs.
Does Nobel Prize exist in Classic Era? Does Solidarity were formed in Medieval? Of course not, but that doesn't prohibited those civs from using those unique abilities!
Does Brazil exist in Renaissance? No, but you don't have to wait until Industrial Era to build all those brazilwood camps, do you?
Of course, this is your own mod, you'll do what you please. Just my two cents, why your argument isn't really valid.
Have a nice day