So, Lightroom and ACR will process RAW pixel shifted images, but any place there is even a tiny amount of movement in the image, they will produce artifacts. If you wish to have motion correction in the image the top options are the Digital Camera Utility (DCU) that is put out with Pentax cameras and Raw Therapee, which is free and downloadable from the interwebs.
I use pixel shift quite a bit and my typical process is to run my DNGs through Raw Therapee to generate a TIFF file that I then finish processing in Lightroom.
This is a crocus shot with pixel shift. There wasn't very much movement as it was a still day, but there was just a little bit of artifact that I could see along the edges and using Raw Therapee took care of that. Processing it directly in Lightroom would have magnified those artifacts.