Differences in quality between a PhD with graduate course work, and one purely on research? The UK PhD programs are based upon just research for three years, whereas in the US there tends to be substantial graduate course work included. 

How does this difference affect the quality of the PhD thesis, and the quality of work produced in the long term?
When someone earned successfully and honestly his PhD in a good research group, either in the US system or in UK/Germany (Master degree is often mandatory for starting PhD), there will probably be no strong differences in the overall quality, I wouldn't make here any generalizations based on this fine system nuances. The level and depth of research experience are very similar (also STEM students in Germany don't work on average 80-90 hours a week, 60 will be rare ;))

But, when a student did choose a distinct topic and research field for his master and PhD thesis, you can be a bit more sure he is really motivated for this work and research generally, while a US PhD student with a bachelor (and without master) maybe is just trying to finish what he started over the years, in spite of vanishing interest/motivation in research generally (see link above) or that distinct topic. During the short time of a bachelor thesis you cannot find out, if you are suited for research and a distinct field in my opinion. In Germany it's hard to get invitations to PhD job interviews at all without a master thesis near to a given research project. Motivation and background is here more important than 0,5 better grade or 3 year younger age. In interviews they mostly check, how motivated, interested, knowledgable is a candidate for that distinct field. So there will probably be no big differences in quality, but you can be more sure about long term motivation and therefore originality/quality of his research.

As we currently have a (another) case of plagiarism in Germany (our education minister obviously wasn't trained, e.g. by a bachelor nor master thesis, for writing a long PhD thesis correctly), I have to add that somebody who has written a bigger master and PhD thesis will also have more practice in publishing, citing, researching literature...

Side note: Personally, I think the german system is more selective, while the US system can afford this system because of a abundance of PhD students and applicants (thats also the reason they have to work 80-90 instead of 60 hours, competition being stronger and teaching of undergraduate students in Germany needs very good command of german language, we are limited in hiring foreign students for those jobs). A very good master and PhD thesis is a strong hallmark for the motivation of a student and future researcher for a distinct research field.