<p>Heroic Spirits and the Throne of Heroes exist outside of the time axis and the different timelines and all that, yes. However, Fate/EXTRA and its sequels are not summoning from the Throne of Heroes, but the records of the Moon Cell so there isn't any direct continuity between the EXTRA versions of the Servants and the FSN versions, with the exception of Artoria due to her unique summoning circumstances in FSN.
</p><p>The Wiki actually <i>did</i> have separate pages for the EXTRA versions of Cu Chulainn and Karna until very recently and still has a separate page for Gilgamesh. Honestly, I think merging the Cu and Karna pages was a strange move and I don't...entirely see the logic behind it. If we are merging alternate versions of characters because they are <i>technically</i> the same person, we should probably do the same for all of these GO variants that are basically "the exact same character, but in a different class" or "the same character, but younger". (Saber Lily was even merged with Artoria proper until GO despite GO being clear they are the same character at different points in life)
</p><p>I haven't watched the anime up to that point (if it's gotten there), but if I recall, the Giles who appears initially appears as Jeanne knew him (using the design that GO would later use as his Saber design) and then 'morphs' into his Caster design to show how depraved he became.
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