Lex would have his own "No More Mutants" moment (see Luthor's Everymen in 52)
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YES Capes. YES Masks. YES Secret Identities.
I think Lex would have a stance similar to what Doctor Doom expressed in the FF/X-Men mini by Chip Zdarsky... how dare mutants consider themselves superior just because they were born with powers.
Lex Luthor hates Superman because Superman is more popular than him, it's a hatred born of jealousy. The fact that mutants are hated would mean Lex would not hate them, instead, he would see them as a resource to exploit.
Yeah Genoshan Magistrates... that.. that's what Lex would do.