I was putting some more thought into the role of the SCH soulstone as home to the Fairy. SCH are an extension of ACN, and one major difference between entities summoned by ACN and SMN, and those summoned by SCH, is that the SCH summons apparently persist even when not summoned. They do not completely vanish between summonings, and maintain a continuity of memory between summons. Carbuncles (and likely also Egis), on the other hand, are created wholly anew each time they are summoned, and do not have any memories from their times previously summoned.

It makes me wonder if early Scholars might not have originally summoned Fairies just as Arcanists do Carbuncles, with the Fairy completely disappearing and "resetting" between each summoning. Eventually, Scholars realized that it could be strategically useful for their Fairies to exist persistently, even when not actively summoned. There may have been many experiments to find ways to preserve Fairies between summonings before finally settling on storing the Fairy within the Scholar Soulstone.

Otherwise, we start running into chicken-or-the-egg issues... If you can't be a SCH without a Soulstone, where did the first Fairies come from?