You can take JPEG pixel shift images right in the camera with the K-3II. You don't need to use PP at all. DCU will sharpen the RAW PS images, and you can use the RAWs in ACR/Lightroom. Or use a special version of dcraw, which may be incorporated in the various other programs that use dcraw, I dunno. Image Resource did one the better analyses:
Pentax K-3 II gallery: Pixel Shift Resolution goes head-to-head in the real world!
I can't see why PS can't be used in APS-C mode. Shouldn't matter what's in front of the sensor. But again, the mode may not be as smart as to pick out an individual quivering leaf and using just one image for that, while using all four for the other parts of the picture. But maybe. And the pixel shift itself is so tiny it could mean that it might be very difficult for an algorithm to pick out what to stack and what to mask; see the thread here:
https://www.pentaxforums.com/forums/172-pentax-k-3/311865-pixel-shift-finicky.html
In that thread some used dcraw PS to pick apart motion affected pixels, and you can see depending on where you set the threshold you can get movement most anywhere; thermal movement in the air can trigger it. And then there's file size, etc. I wouldn't expect wonders; for many K-3II users it isn't worth the hassle to use outdoors much. So check out the info there if the PS technology is high on your list of why to buy the K-1.