It's difficult to say without seeing the guitar in the flesh. My first reaction would to be to give the truss rod a small tighten and raise the strings slightly to compensate (and repeat as necessary). The truss rod doesn't affect the top few frets, so the overall bridge height is often driven by how well you can bend on the higher frets. If you raise the saddles, then you can straighten the neck to compensate. You don't want a convex/back curve in the neck, but you can go right down to flat (especially as you've levelled the frets).

I have got a couple of guitars where I've reduced the height of the last few frets in order to stop choking, but that's from bending higher up the neck, at the 17th fret,not from the 12th and it was normally over a tone's bend before that happens. And they were 7.25" radius necks which will choke out more easily. The standard PBG neck radius is 12", so there shouldn't be choking problems.