My two cents:
As a long-time commissioner, I would NOT want the headache of monitoring daily starting lineups, regarding Ohtani. Given that constraint, there are two realistic options.
Allow only one version (hitter or pitcher) to be drafted, or protected. Once the first version is selected, the other version is no longer eligible.
Allow both versions to be drafted/protected as separate entities. They would be treated as separate players. You could play both at the same time. The Angels would have to use two protects to grab both. It would be possible for the Angels to protect the hitter and for a different team to draft the pitcher and vice versa (or even for both versions to get drafted by one or two teams).
It would be fun to see Ohtani face Ohtani.