I have found the cause for it, I don't know if it's intentional or not, but forming the byzantine empire doesn't grant the T1 reform "byzantine autocracy" which enables the subject type, so that's why they aren't available. Also, because of this, the mission "recover authority" doesn't grant the upgraded T1 reform "Reformed Byzantine Monarchy" which also enables the subject type.
So on the chance that this is unintentional it can be fixed by modifying the decision to "Restore the Byzantine Empire" by adding that it grants the byzantine T1 reform.