The PEP allows a whl upload to supersede a previous rim upload, but doesn’t state explicitly whether that deletes the previous upload or not. Requiring automatic deletion of the superseded file would eliminate the ambiguity.
That said, I find @pf_moore and @steve.dower’s points persuasive - this feels like a case where any effort invested is likely to be somewhat flexible in the implementation goals it targets, and improving the ergonomics of querying and hosting secondary indexes would offer a better overall outcome.