Is it okay to let body text follow immediately after intermediate level headings?
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.