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Welcome to purgatory neethree
First off, the gameboard and the metaworld are two separate things. You can think of the gameboard as the stage and the metaworld as the backstage. Usually metaworld places can be distinguished from the gameboard places because they have that purplish light and swirls.
As for what the gameboards are, there are mainly two different theories, one is that they are "kakera" a la Higurashi. In other words alternate realities.
However since EP5 and even more with EP6 a completely different theory has become dominant, but it's better if you learn about that at least after you read EP5.
Don't worry too much about magic, it is commonly accepted that the magic explanations do not make much sense once you think deep about them. It is probably done so by Ryuukishi so by noticing that you understand that the "fantasy" perspective isn't really going to explain anything.
About Virgilia in EP3, she was killed by Beatrice actually, but of course later you learn that it was just a charade. Beatrice however was killed by the siestas, but notice that both Virgilia and Beatrice were simply killed as pieces on the gameboard, they are still alive and well in the metaworld... if it's allright to say that metacharacters are "alive". It's probably better to say that metacharacters exist.
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