Is it okay to let body text follow immediately after intermediate level headings? Let's say we have a thesis/scientific paper with a sectioning depth of three [chapter, section, subsection]. I already often wondered: 

Is it okay to have text outside of the lowest level, i. e. subsections?

For instance giving the introduction to / overview of a chapter is that done right after the chapters headline (or sections headline) or in the first subsection appearing in the same chapter?
In my view, it is perfectly acceptable. It often helps readability, and logically it makes sense (a good example is the "introduction before subsections" that you cited).

That said, some people hate it, and I have already encountered referees who wanted me to change it. I haven't been able to infer a reasonable motivation up to now, so I would be interested in reading arguments in its favor.

Academic papers typically have no table of contents, so there is even less motivation for enforcing a strict tree-like structure.