Hello @heckflosse
I’m a Nikon guy myself, though I would still prefer a pixelshift-capable cam for your usecase.
One downside of this choice is the biggest size of the Raw files (judging only from what I have read of course and I may be completely wrong here…). Therefore, much time to process them in the camere itself; much time to download them; much time to edit them etc.
In truth, I am sure I am going to miss my Nikon D700 a lot 
When I take my macro pictures of plant diseases, very close to the subject, I am always forced to focus stacking them (in short take many pictures) in order to assemble them later on with another software (now my workhorse is Affinity photo but I have tried also Zerene which was a magnificent software at this task). As a consequence, I suspect the pixel shifting feature is not good enough for this task (but again, I may be 100% wrong…)
But indeed, I am persuaded the Pentax choice is a very good option as well