I can probably shed some light on this topic to a degree. I don't have a K3II nor am I going to order one, but have read the II's user manual, and inadvertently done some similar imaging to a degree.
Last weekend I was re-post processing a set of images from a couple of years ago. Sunset and Sunrise images shot at ISO 80 for the best image quality I could get, and bracketed (5 images +/-2ev). The problem was that the object I was shooting had some slight movement to it. She was a square rigged ship tied up to a pier. She did not appear to be affected by wind or the tide, but the images showed otherwise. Also, when the ship was stable, the rigging was bouncing around like a banjo string, just moving a cm or so - not much, but just enough.
Stacking the images (using a HDR utility) produced a blob, however quickly sequencing through them (cartoon mode) showed the ship ever so slightly moving around. Going into each individual image (especially the -1 and -2 ev frames) showed on some the rigging slightly moving - a fraction of an inch - essentially producing a "halo" effect around the line. Other times, one of the masts was moving and had a blur to it.
On others, you could clearly see the surrounding structures, the dock, the buildings, etc. were rock solid perfect, but the ship was ever so slightly in motion. Now out quite a few images taken, some were just total losses (in particular the over exposed +1, +2 ev frames). Others were mostly OK, but had isolated problems. Finally, there were about a dozen (out of several hundred), where I caught the ship just right, with everything still for that moment. Those were the keepers that I was able to really rescue. The more I post processed - especially the really under exposed ones (obviously with the shortest shutter speed), lighten up, adjust the lights, darks, shadows, highlights, contrast and over all exposure a bit, the various problems popped out - or didn't show up.
So, in terms of capturing the images using Pixel Shifting, the manual says the physical shutter opens, and then using the electronic shutter capability, 4 images will be taken with the same exposure, then combined producing a fifth, then all five saved to the "new" file format. The supplied Pentax software will un-bundle the "new" file format and provide the individual files for what ever further processing you desire.
If there is some movement in one area of the image, you are just going to have to judge if its acceptable or not. If it's way in the background with a touch of blur - most will never see it, and if you and they do, does it detract sufficiently from the overall image to render it not useable. In the end, it's your call. You are the photographer.