The bug here appears to be that HL is allowing you to take additional metagenetic qualities if you take a metavariant - you're supposed to have to take the Changling quality, even if you're already a metavariant, in order to allow the purchase of additional metagenetic qualities.
If you do take Changeling for a metavariant, the free qualities from your metavariant don't count against Changeling's limits, nor do those free qualities from your metavariant count against the normal positive/negative quality limits.
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