To what extent should a reader be required to read a paper to understand a chapter?
The flow of thesis differs in preference from one supervisor to another. The specification provided by your supervisor doesn't seem unreasonable. In fact, I would endorse it myself. 

It is natural for most readers to skip the introduction and just cut to the chase. Readers would be particularly interested in the implementation and results. Although that doesn't mean introduction isn't mandatory. You just have to minimise the dependency between the main matter and the introductory matter. The lesser you make the reader to turn back pages, the better would be the reading experience.