Both preferred multiple alternatives for nominative case (“it/she”) and preferred single alternatives for nominative and accusative case (“she/her”) are commonly used. When at least one of the pronouns involved are traditional pronouns rather than neopronouns this is pretty clear as to which is being used (though unless they are both standard pronouns, its ambiguous as to the accusative case to use with the neopronoun, but of course it indicates that the standard pronoun and its corresponding accusative form are acceptable, so that’s not really a problem), though if they are both neopronouns it might be ambiguous in theory (in practice, if they are both neopronouns, its always the second nominative/accusative form, not the multiple alterantives form.) Occasionally, you’ll find neopronouns presented in a triplet where the third is possessive case (which really should always be the case with neopronouns, since otherwise you’re left to conjure up your own possessive if one is needed.)

No, you misunderstand. You need to apply some common sense, not rigorous logic.

“they/he” and “it/she” indicate alternatives, whereas “she/her” indicates different cases.

That.....frankly doesn't make sense, or it breaks the English language in ways that I'm not familiar with(admittedly it's not my first language).

Do you mean that instead of saying "it's her apple" you'd say "it's she apple"?