I think the phase detection elements should show up. That is, I suppose they are being used for imaging. If they are not used for imaging, they might be missing, or they might still be there, in the raw channels I'm examining. That would be visible.
But if they are shown one way or the other, holding a card in front of half the lens should make the phase detection pixels aimed at that half darker. That's the principle I'm trying to exploit.
Like it says in the article jerryy cited, "Fujifilm's system provides a seemingly simple solution - masking-off half of a sensel means it only receives light from one side of the lens. By creating strips of these sensels, half 'looking' one way, half 'looking' the other, the camera gets the two distinct images necessary for phase detection AF." Though, "strips" doesn't sound right, I think they'd just be pairs, one pair at each focus point. Then again, they're talking about tens of thousands of these, not a few hundred (two for each focus point). Still trying to figure out what's up here....