Isabella is closer to a 'Meritocrat' than a 'True' Metahuman Supremacist. She dangles Metahuman Supremacy and an All-Metahuman world to her followers, but what she actually wants is a pyramid-like apertheid in which a small minority, like her, is at the top, with the apples being a 'safety valve' to allow the most talented of those below to be inducted into the Metahuman minority, as well as a string to bait the more 'idealistic' Metahuman Supremacists into relying on her to create a world friendlier to Metas. Basically, as mentioned, the Fruits are a limited supply of bargaining chips that deceive people into thinking an all-metahuman future is around the corner, when it's really not.
That's why the 'Eden Plan' is complicated and relies heavily on specifics; the Big Bad wants to convince her followers that she wants to create New Metas and perfect healing for the Metas already under her allegiance, but at the same time wants to limit the supply of New Metas and perfect healing to preserve her rule.
If the Reformists were willing, they /could/ synthesize a serum/prion/virus from the fruit, but they would only do so if they can be successfully convinced that the continued existence of Baseline Humans is a threat to them; therefore, if Eden truly agreed with the Underground's goals, then he would stick with the Reformists and their International reach.
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