There are cases in which both indicative and subjunctive work, though with a subtle difference of meaning. In this specific case, in which identity is involved:
(1) ... quién sea él.
(2) ... quién es él.
one thing is clear: he does have an identity (a name, a role), which the speaker is not interested in discovering or in considering.
To understand the difference above, let's see a different pair of sentences:
- No me importa que llueva. (We don't know if it's raining.)
- No me importa que llueve. (We know it's raining.)
We can thus see that the subjunctive casts some doubt as to the truth of the clause, while the indicative provides certainty.
If we apply this distinction to your pair of sentences, if the speaker uses (1) he wants to imply that he is not willing to believe that the other person is who he claims to be. If the speaker uses (2), he implies that he will not challenge his identity, hierarchy, authority, etc.
As a result, sentence (1) may be more pejorative: the speaker does not care who he is and, even if he finds out, he indicates that he is reluctant to believe it.