First of all, because the converter makes a mod for EU4 out of a CK2 save rather than just trying to turn it into an EU4 save, flags and countries are all preserved easily. Secondly, I'm not convinced that the devs really meant that the Roman Empire has its own set of unique ideas. I believe the question was whether they used generic ideas or had their own, and I suspect by the reply "they have their own" the devs meant that they would use the Byzantium national ideas. That's what I'm going to continue to believe until either I see it in-game or one of the devs categorically states that the Roman Empire uses different national ideas to Byzantium.