The STATEMENT MADE BY NATIVES:
Be is not transitive.
This part is correct. Be is certainly not a transitive verb; be is an auxiliary verb.
that’s why “Whom can he be?” and “Who can be him?” are wrong.
This may be a statement made by some natives, but it's wrong. And not all natives say it. So forget that part. And ignore those failed examples. They're wrong to start with, and don't exemplify anything.
So, the reason why I don’t want to be him is correct is not because be is transitive, but rather because him is the basic form of the 3rd person singular masculine pronoun. This may be surprising; many people have been told that he is the pronoun and him is for objects only. This is no longer true, if it ever was.
He is a special form used only for subjects of tensed clauses; any other (non-possessive) use gets him (similar remarks for the pronoun pairs me/I, her/she, us/we, and them/they). These used to be case-form variants, like German pronouns, but unlike German, English doesn't have cases for nouns at all, and they've pretty much disappeared in English pronouns, too.
That's why Him and me are gonna go together is a normal thing to say. Neither I nor he is really comfortable in a conjoined NP, so me and him pop up naturally. Similarly, when a pronoun is a predicate nominal, you get him, as in I wouldn't want to be him.
Of the examples given, neither (1) nor (2) are correct; (2) is ungrammatical, and (1) doesn't make sense unless the predicate be him is taken metaphorically, to refer (for instance) to an actor playing some historic figure:
- What about Hitler? Who can be him?
The rest of the question is unclear; it makes too many assumptions.