My revised workflow:
1. Shoot a pixel shift RAW image with the K-1
2. Open the file in RAW-Therapee
3. Under 'Processing Profiles' you will see 'last saved' click on this arrow
4. Now you will see "bundled profiles" click, then click (pixel shift) then click "PS ISO Low" (I used 100 ISO in camera)
5. Finish post processing as normal
6. Go to the 'Color' icon, click and go to the bottom and choose your color output profile
7. Save in 16 bit TIFF
Here are three images from Flickr: first the entire scene, second and third are crops (second no pixel shift, third with pixel shift):
Pentax K1 Pixel shift | The large image is the scene, of the? | Flickr Pentax K1 Pixel shift | The large image is the scene, of the? | Flickr Pentax K1 Pixel shift | The large image is the scene, of the? | Flickr
The Pixel Shift crop looks a little over sharpened, I'll have to do more research. Any further suggestions?