I am generally not in favour of the idea that lower-level headings should be progressively indented. (But publishers are entitled to set their own styles and you should follow them.)
In my opinion, you should create headings that are distinguished by 'type style and placement' (cf. Chicago Manual of Style, 16th ed, §.1.54). I'd add: but the lower the level of heading, the less distinguishable it should be from the main text. That is, sectional headings should be designed hierarchically -- say, chapter-level headings in a larger and different and bold font and centred on the line; section-level headings in a bold font and centred; subsection-headings in italics; etc. To me, this means I'm more inclined to have low-level headings flush left than higher level ones (e.g., I will centre a chapter heading and not a subsection heading, but I probably wouldn't do the reverse).
The numbering is useful to denote hierarchy, but, strictly speaking, it is only really adding value if you are going to refer to different (sub-)sections (e.g.,
see section 1.5.3, above). Otherwise, some tasteful, careful, and subtle design choices will do just the trick and readers are likely to implicitly pick up on it.
Generally speaking, for sober documents where numbered sections are useful and common, a 'less is more' approach to typesetting and typography is often best.