What causes incorrect PDFkit or blurry PDF display in macOS Sierra and how to fix or remedy that situation?
The answer to this question involves a bunch of things. 


Preview/PDFKit in Sierra is just buggy (10.12.5 +.6 Preview Version 9.0 (909.18)). It is less robust in this regard as Preview in either Yosemite or High Sierra. And coupled with apparent auto-termination this is the only 'background process' that really matters in this regard.
Once the bug gets triggered (enough) it is much earlier in Sierra Preview compared to other versions and propagates through the application: that vanishes from the Dock  or from the Cmd+Tab  application switcher but remains active in the background as Activity Monitor will show.
That tempted to reach the conclusion that almost all PDFs were affected at first. But once a killall Preview cleared that process up for good, only bug-triggering PDFs (that might justifiably called substandard) really triggered that behaviour.
But one such concrete bug trigger I could positively identify is related to Multiple PDFs with page group included in a single page warning. 
It is somehow dependent on the number of these incorrect inclusion attributes but I couldn't determine the exact amount.
Since many of my own PDFs, files I downloaded and had to work with and also the given example in the Question above demonstrate: this is a widespread weakness leading to very unwanted behaviour on Sierra, not only but (for me) mostly from LaTeX generated content or many includes for an assembled PDF.


Unless this bug in Preview is fixed, or the PDFs are reflown there is no solution but to avoid Preview on Sierra for these kind of files. 

A workaround is to use other applications like Acrobat Reader from the start for all PDFs to display if they contain text.

Once this bug is triggered with Preview, it is necessary to kill all PDFkit related processes since quitting the application Preview via cmd+q or the equivalent menu item is not enough sufficient.