Okay, I'm surely missing something here. Or am I?
The present "prelate" of Opus Dei is not a bishop, but a priest, Fr Ocariz. He is termed "prelate" even though he is not a bishop, is that right? The previous two prelates were bishops. So is Francis saying "you may have had bishops in the past, but you won't going forward, your prelate will simply be a priest and not a bishop"?
And I'm assuming that he could do likewise if the SSPX ever became a personal prelature. (FWIW, and probably pretty much everybody here is aware of this, the Superior General of the SSPX need not be a bishop, can be, but doesn't have to be.)
I don't know who the present "prelate" is. If it is a priest, then you are correct in stating something about this article doesn't make sense. Perhaps the latest change is not the clerical status of the prelate leader, but that the oversight is no longer the Congregation of Bishops, but the Dicastery for the Clergy?
As for the SSPX, I wonder, with this move, whether Bergoglio is opening the way for a prelature for them.