How much knowledge is expected of a PhD applicant as compared to a postdoc or a research assistant?
I will only attempt a partial answer here as your question is a bit convoluted. Doctoral students on the first day, are expected to know less than a post-doc or research assistant on the first day. But they are expected to know relevant things. How your specific case would be judged would be up to a specific judge (i.e. a potential advisor). 

But note that universities (as opposed to commercial/industrial labs) have a dual purpose. It isn't just to support the research interests of the current faculty, but to also educate the next generation(s) of scholars and researchers. Without that second  purpose there would be no need for graduate students at all. But then scholarship would end in a generation or two. 

Universities are long term contributors to the future and take the role seriously, both in research and teaching. 



The other links in your question seem to be pretty good for answering your other concerns.